mkdir /home/userid/Documents/amber10/bin /home/userid/Documents/amber10/lib /home/userid/Documents/amber10/include
mkdir: cannot create directory `/home/userid/Documents/amber10/bin': File exists
mkdir: cannot create directory `/home/userid/Documents/amber10/lib': File exists
mkdir: cannot create directory `/home/userid/Documents/amber10/include': File exists
make: [install] Error 1 (ignored)
(cd ucpp-1.3 && make install )
make[1]: Entering directory `/home/userid/Documents/amber10/src/ucpp-1.3'
Makefile:35: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
mv ucpp /home/userid/Documents/amber10/bin
make[1]: Leaving directory `/home/userid/Documents/amber10/src/ucpp-1.3'
(cd byacc && make install )
make[1]: Entering directory `/home/userid/Documents/amber10/src/byacc'
mpicc -c -m64 -DBINTRAJ -DMPI  -o closure.o closure.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o error.o error.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o lalr.o lalr.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o lr0.o lr0.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o main.o main.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o mkpar.o mkpar.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o output.o output.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o reader.o reader.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o skeleton.o skeleton.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o symtab.o symtab.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o verbose.o verbose.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o warshall.o warshall.c
main.o: In function `create_file_names':
main.c:(.text+0x62f): warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
mv yacc /home/userid/Documents/amber10/bin
make[1]: Leaving directory `/home/userid/Documents/amber10/src/byacc'
(cd carpack && make install );
make[1]: Entering directory `/home/userid/Documents/amber10/src/carpack'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dgetv0.o dgetv0.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlaqrb.o dlaqrb.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dnaitr.o dnaitr.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dnapps.o dnapps.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dnaup2.o dnaup2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dnaupd.o dnaupd.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dnconv.o dnconv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dneigh.o dneigh.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dneupd.o dneupd.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dngets.o dngets.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsaitr.o dsaitr.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsapps.o dsapps.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsaup2.o dsaup2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsaupd.o dsaupd.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsconv.o dsconv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dseigt.o dseigt.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsesrt.o dsesrt.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dseupd.o dseupd.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsgets.o dsgets.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsortc.o dsortc.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsortr.o dsortr.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dstatn.o dstatn.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dstats.o dstats.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dstqrb.o dstqrb.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsarpack.o dsarpack.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o wallclock.o wallclock.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dmout.o dmout.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o ivout.o ivout.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dvout.o dvout.c
ar rv arpack.a dgetv0.o dlaqrb.o dnaitr.o dnapps.o dnaup2.o dnaupd.o dnconv.o dneigh.o dneupd.o dngets.o dsaitr.o dsapps.o dsaup2.o dsaupd.o dsconv.o dseigt.o dsesrt.o dseupd.o dsgets.o dsortc.o dsortr.o dstatn.o dstats.o dstqrb.o dsarpack.o wallclock.o dmout.o ivout.o dvout.o
ar: creating arpack.a
a - dgetv0.o
a - dlaqrb.o
a - dnaitr.o
a - dnapps.o
a - dnaup2.o
a - dnaupd.o
a - dnconv.o
a - dneigh.o
a - dneupd.o
a - dngets.o
a - dsaitr.o
a - dsapps.o
a - dsaup2.o
a - dsaupd.o
a - dsconv.o
a - dseigt.o
a - dsesrt.o
a - dseupd.o
a - dsgets.o
a - dsortc.o
a - dsortr.o
a - dstatn.o
a - dstats.o
a - dstqrb.o
a - dsarpack.o
a - wallclock.o
a - dmout.o
a - ivout.o
a - dvout.o
ranlib arpack.a
mv arpack.a /home/userid/Documents/amber10/lib
make[1]: Leaving directory `/home/userid/Documents/amber10/src/carpack'
(cd clapack && make install )
make[1]: Entering directory `/home/userid/Documents/amber10/src/clapack'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsyev.o dsyev.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsyevd.o dsyevd.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dormtr.o dormtr.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dormql.o dormql.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dormqr.o dormqr.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlansy.o dlansy.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsytrd.o dsytrd.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dorgtr.o dorgtr.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsteqr.o dsteqr.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsterf.o dsterf.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlascl.o dlascl.c
mpicc -c -O0 -o dlamch.o dlamch.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o ilaenv.o ilaenv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlassq.o dlassq.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsytd2.o dsytd2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dorm2l.o dorm2l.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlatrd.o dlatrd.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dorgql.o dorgql.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dorgqr.o dorgqr.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlasrt.o dlasrt.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlaset.o dlaset.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlanst.o dlanst.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlaev2.o dlaev2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlasr.o dlasr.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlapy2.o dlapy2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlartg.o dlartg.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlae2.o dlae2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dorg2r.o dorg2r.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlarft.o dlarft.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlarfb.o dlarfb.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dorg2l.o dorg2l.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlarfg.o dlarfg.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlarf.o dlarf.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dspev.o dspev.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlansp.o dlansp.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsptrd.o dsptrd.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dopgtr.o dopgtr.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dposv.o dposv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dppsv.o dppsv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dspsv.o dspsv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dgeev.o dgeev.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsptrs.o dsptrs.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsptrf.o dsptrf.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dpptrs.o dpptrs.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dpptrf.o dpptrf.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dgebak.o dgebak.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dtrevc.o dtrevc.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlacpy.o dlacpy.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dhseqr.o dhseqr.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dorghr.o dorghr.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dgehrd.o dgehrd.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dgebal.o dgebal.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlange.o dlange.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlabad.o dlabad.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlahqr.o dlahqr.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlarfx.o dlarfx.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlanhs.o dlanhs.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlaln2.o dlaln2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dgehd2.o dgehd2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlahrd.o dlahrd.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlanv2.o dlanv2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dladiv.o dladiv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dgerq2.o dgerq2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dorm2r.o dorm2r.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlarnv.o dlarnv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dgeqr2.o dgeqr2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlaruv.o dlaruv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dspevd.o dspevd.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dstedc.o dstedc.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dopmtr.o dopmtr.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlaed0.o dlaed0.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlaed1.o dlaed1.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlaed7.o dlaed7.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlaeda.o dlaeda.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlaed8.o dlaed8.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlaed9.o dlaed9.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlamrg.o dlamrg.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlaed2.o dlaed2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlaed3.o dlaed3.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsygv.o dsygv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsygst.o dsygst.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsygs2.o dsygs2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlaed4.o dlaed4.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlaed5.o dlaed5.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dlaed6.o dlaed6.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dpotrf.o dpotrf.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dpotrs.o dpotrs.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dpotf2.o dpotf2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o ieeeck.o ieeeck.c
ar rv lapack.a dsyev.o dsyevd.o dormtr.o dormql.o dormqr.o dlansy.o dsytrd.o dorgtr.o dsteqr.o dsterf.o dlascl.o dlamch.o ilaenv.o dlassq.o dsytd2.o dorm2l.o dlatrd.o dorgql.o dorgqr.o dlasrt.o dlaset.o dlanst.o dlaev2.o dlasr.o dlapy2.o dlartg.o dlae2.o dorg2r.o dlarft.o dlarfb.o dorg2l.o dlarfg.o dlarf.o dspev.o dlansp.o dsptrd.o dopgtr.o dposv.o dppsv.o dspsv.o dgeev.o dsptrs.o dsptrf.o dpptrs.o dpptrf.o dgebak.o dtrevc.o dlacpy.o dhseqr.o dorghr.o dgehrd.o dgebal.o dlange.o dlabad.o dlahqr.o dlarfx.o dlanhs.o dlaln2.o dgehd2.o dlahrd.o dlanv2.o dladiv.o dgerq2.o dorm2r.o dlarnv.o dgeqr2.o dlaruv.o dspevd.o dstedc.o dopmtr.o dlaed0.o dlaed1.o dlaed7.o dlaeda.o dlaed8.o dlaed9.o dlamrg.o dlaed2.o dlaed3.o dsygv.o dsygst.o dsygs2.o dlaed4.o dlaed5.o dlaed6.o dpotrf.o dpotrs.o dpotf2.o ieeeck.o dsyevd.o dormtr.o dormqr.o dormql.o dorm2l.o 
ar: creating lapack.a
a - dsyev.o
a - dsyevd.o
a - dormtr.o
a - dormql.o
a - dormqr.o
a - dlansy.o
a - dsytrd.o
a - dorgtr.o
a - dsteqr.o
a - dsterf.o
a - dlascl.o
a - dlamch.o
a - ilaenv.o
a - dlassq.o
a - dsytd2.o
a - dorm2l.o
a - dlatrd.o
a - dorgql.o
a - dorgqr.o
a - dlasrt.o
a - dlaset.o
a - dlanst.o
a - dlaev2.o
a - dlasr.o
a - dlapy2.o
a - dlartg.o
a - dlae2.o
a - dorg2r.o
a - dlarft.o
a - dlarfb.o
a - dorg2l.o
a - dlarfg.o
a - dlarf.o
a - dspev.o
a - dlansp.o
a - dsptrd.o
a - dopgtr.o
a - dposv.o
a - dppsv.o
a - dspsv.o
a - dgeev.o
a - dsptrs.o
a - dsptrf.o
a - dpptrs.o
a - dpptrf.o
a - dgebak.o
a - dtrevc.o
a - dlacpy.o
a - dhseqr.o
a - dorghr.o
a - dgehrd.o
a - dgebal.o
a - dlange.o
a - dlabad.o
a - dlahqr.o
a - dlarfx.o
a - dlanhs.o
a - dlaln2.o
a - dgehd2.o
a - dlahrd.o
a - dlanv2.o
a - dladiv.o
a - dgerq2.o
a - dorm2r.o
a - dlarnv.o
a - dgeqr2.o
a - dlaruv.o
a - dspevd.o
a - dstedc.o
a - dopmtr.o
a - dlaed0.o
a - dlaed1.o
a - dlaed7.o
a - dlaeda.o
a - dlaed8.o
a - dlaed9.o
a - dlamrg.o
a - dlaed2.o
a - dlaed3.o
a - dsygv.o
a - dsygst.o
a - dsygs2.o
a - dlaed4.o
a - dlaed5.o
a - dlaed6.o
a - dpotrf.o
a - dpotrs.o
a - dpotf2.o
a - ieeeck.o
a - dsyevd.o
a - dormtr.o
a - dormqr.o
a - dormql.o
a - dorm2l.o
ranlib lapack.a
mv lapack.a /home/userid/Documents/amber10/lib
make[1]: Leaving directory `/home/userid/Documents/amber10/src/clapack'
(cd cblas && make install )
make[1]: Entering directory `/home/userid/Documents/amber10/src/cblas'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dasum.o dasum.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o daxpy.o daxpy.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dcopy.o dcopy.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o ddot.o ddot.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dgbmv.o dgbmv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dgemm.o dgemm.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dgemv.o dgemv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dger.o dger.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dnrm2.o dnrm2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o drot.o drot.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o drotg.o drotg.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsbmv.o dsbmv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dscal.o dscal.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dspmv.o dspmv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dspr.o dspr.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dspr2.o dspr2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dswap.o dswap.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsymm.o dsymm.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsymv.o dsymv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsyr.o dsyr.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsyr2.o dsyr2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsyr2k.o dsyr2k.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dsyrk.o dsyrk.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dtbmv.o dtbmv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dtbsv.o dtbsv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dtpmv.o dtpmv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dtpsv.o dtpsv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dtrmm.o dtrmm.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dtrmv.o dtrmv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dtrsm.o dtrsm.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dtrsv.o dtrsv.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o idamax.o idamax.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o lsame.o lsame.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o xerbla.o xerbla.c
ar rv blas.a dasum.o daxpy.o dcopy.o ddot.o dgbmv.o dgemm.o dgemv.o dger.o dnrm2.o drot.o drotg.o dsbmv.o dscal.o dspmv.o dspr.o dspr2.o dswap.o dsymm.o dsymv.o dsyr.o dsyr2.o dsyr2k.o dsyrk.o dtbmv.o dtbsv.o dtpmv.o dtpsv.o dtrmm.o dtrmv.o dtrsm.o dtrsv.o idamax.o lsame.o xerbla.o
ar: creating blas.a
a - dasum.o
a - daxpy.o
a - dcopy.o
a - ddot.o
a - dgbmv.o
a - dgemm.o
a - dgemv.o
a - dger.o
a - dnrm2.o
a - drot.o
a - drotg.o
a - dsbmv.o
a - dscal.o
a - dspmv.o
a - dspr.o
a - dspr2.o
a - dswap.o
a - dsymm.o
a - dsymv.o
a - dsyr.o
a - dsyr2.o
a - dsyr2k.o
a - dsyrk.o
a - dtbmv.o
a - dtbsv.o
a - dtpmv.o
a - dtpsv.o
a - dtrmm.o
a - dtrmv.o
a - dtrsm.o
a - dtrsv.o
a - idamax.o
a - lsame.o
a - xerbla.o
ranlib blas.a
mv blas.a /home/userid/Documents/amber10/lib
make[1]: Leaving directory `/home/userid/Documents/amber10/src/cblas'
(cd f2c &&  make install  )
make[1]: Entering directory `/home/userid/Documents/amber10/src/f2c'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o abort_.o abort_.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_atan.o d_atan.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_cosh.o d_cosh.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_int.o d_int.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_nint.o d_nint.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_sinh.o d_sinh.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_abs.o d_abs.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_atn2.o d_atn2.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_dim.o d_dim.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_lg10.o d_lg10.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_prod.o d_prod.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_sqrt.o d_sqrt.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o exit_.o exit_.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_acos.o d_acos.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_exp.o d_exp.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_log.o d_log.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_sign.o d_sign.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_tan.o d_tan.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_asin.o d_asin.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_cos.o d_cos.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_mod.o d_mod.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_sin.o d_sin.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o d_tanh.o d_tanh.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o wsfe.o wsfe.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o s_cmp.o s_cmp.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o s_copy.o s_copy.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o s_paus.o s_paus.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o s_rnge.o s_rnge.c
s_rnge.c: In function ‘s_rnge’:
s_rnge.c:16: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘ftnint’
s_rnge.c:19: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘int’
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o s_stop.o s_stop.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o wsle.o wsle.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o xwsne.o xwsne.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o util.o util.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o wref.o wref.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o wrtfmt.o wrtfmt.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o rsne.o rsne.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o sfe.o sfe.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o sue.o sue.c
sue.c: In function ‘e_wsue’:
sue.c:68: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
sue.c:75: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o uio.o uio.c
uio.c: In function ‘do_us’:
uio.c:23: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
uio.c: In function ‘do_ud’:
uio.c:56: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o open.o open.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o rdfmt.o rdfmt.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o rewind.o rewind.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o rsfe.o rsfe.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o rsli.o rsli.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o ilnw.o ilnw.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o inquire.o inquire.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o lread.o lread.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o fmtlib.o fmtlib.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o ftell_.o ftell_.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o iio.o iio.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o err.o err.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o close.o close.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dfe.o dfe.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o dolio.o dolio.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o due.o due.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o endfile.o endfile.c
endfile.c: In function ‘f_end’:
endfile.c:30: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘ftnint’
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o backspace.o backspace.c
backspace.c: In function ‘f_back’:
backspace.c:44: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o fmt.o fmt.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o sig_die.o sig_die.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o pow_dd.o pow_dd.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o pow_di.o pow_di.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o pow_ii.o pow_ii.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o lwrite.o lwrite.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o i_len.o i_len.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o s_cat.o s_cat.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o F77_aloc.o F77_aloc.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o wsne.o wsne.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -o typesize.o typesize.c
ar rv f2c.a abort_.o  d_atan.o  d_cosh.o  d_int.o   d_nint.o  d_sinh.o d_abs.o   d_atn2.o  d_dim.o   d_lg10.o  d_prod.o  d_sqrt.o  exit_.o d_acos.o  d_exp.o   d_log.o   d_sign.o  d_tan.o d_asin.o  d_cos.o   d_mod.o   d_sin.o   d_tanh.o wsfe.o s_cmp.o s_copy.o s_paus.o s_rnge.o s_stop.o wsle.o xwsne.o util.o wref.o wrtfmt.o rsne.o sfe.o sue.o uio.o open.o rdfmt.o rewind.o rsfe.o rsli.o ilnw.o inquire.o lread.o fmtlib.o ftell_.o iio.o err.o close.o dfe.o dolio.o due.o endfile.o backspace.o fmt.o sig_die.o pow_dd.o pow_di.o pow_ii.o lwrite.o i_len.o s_cat.o F77_aloc.o wsne.o typesize.o 
ar: creating f2c.a
a - abort_.o
a - d_atan.o
a - d_cosh.o
a - d_int.o
a - d_nint.o
a - d_sinh.o
a - d_abs.o
a - d_atn2.o
a - d_dim.o
a - d_lg10.o
a - d_prod.o
a - d_sqrt.o
a - exit_.o
a - d_acos.o
a - d_exp.o
a - d_log.o
a - d_sign.o
a - d_tan.o
a - d_asin.o
a - d_cos.o
a - d_mod.o
a - d_sin.o
a - d_tanh.o
a - wsfe.o
a - s_cmp.o
a - s_copy.o
a - s_paus.o
a - s_rnge.o
a - s_stop.o
a - wsle.o
a - xwsne.o
a - util.o
a - wref.o
a - wrtfmt.o
a - rsne.o
a - sfe.o
a - sue.o
a - uio.o
a - open.o
a - rdfmt.o
a - rewind.o
a - rsfe.o
a - rsli.o
a - ilnw.o
a - inquire.o
a - lread.o
a - fmtlib.o
a - ftell_.o
a - iio.o
a - err.o
a - close.o
a - dfe.o
a - dolio.o
a - due.o
a - endfile.o
a - backspace.o
a - fmt.o
a - sig_die.o
a - pow_dd.o
a - pow_di.o
a - pow_ii.o
a - lwrite.o
a - i_len.o
a - s_cat.o
a - F77_aloc.o
a - wsne.o
a - typesize.o
ranlib f2c.a
mv f2c.a /home/userid/Documents/amber10/lib
make[1]: Leaving directory `/home/userid/Documents/amber10/src/f2c'
(cd c9x-complex && make skip )
make[1]: Entering directory `/home/userid/Documents/amber10/src/c9x-complex'
using built-in (C99) complex.h functionality
make[1]: Leaving directory `/home/userid/Documents/amber10/src/c9x-complex'
(cd cifparse && make install )
make[1]: Entering directory `/home/userid/Documents/amber10/src/cifparse'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
flex -t cifparse.l | sed 's/yy/cifp/g' > lex.cif.c
/home/userid/Documents/amber10/bin/yacc -v -d cifparse.y
sed 's/yy/cifp/g' < y.tab.c > cifp.tab.c
sed 's/yy/cifp/g' < y.tab.h > cifp.tab.h
rm y.tab.c y.tab.h
mpicc -c -m64 -DBINTRAJ -DMPI  lex.cif.c
cifparse.l: In function ‘delete_punctuation’:
cifparse.l:274: warning: assignment makes integer from pointer without a cast
mpicc -c -m64 -DBINTRAJ -DMPI  -Dflex cifp.tab.c
mpicc -c -m64 -DBINTRAJ -DMPI  cifparse.c
cifparse.c: In function ‘ndb_cif_print_item_value’:
cifparse.c:176: warning: format not a string literal and no format arguments
cifparse.c: In function ‘ndb_cif_write_category’:
cifparse.c:287: warning: cast from pointer to integer of different size
cifparse.c: In function ‘ndb_cif_print_formatted_item_value’:
cifparse.c:370: warning: cast from pointer to integer of different size
cifparse.c:388: warning: cast from pointer to integer of different size
cifparse.c: In function ‘ndb_cif_init’:
cifparse.c:470: warning: cast from pointer to integer of different size
cifparse.c: In function ‘ndb_cif_new_datablock’:
cifparse.c:538: warning: cast from pointer to integer of different size
cifparse.c: In function ‘ndb_cif_get_item_value’:
cifparse.c:1478: warning: cast from pointer to integer of different size
cifparse.c:1497: warning: cast from pointer to integer of different size
rm -f cifparse.a
ar rv cifparse.a lex.cif.o cifp.tab.o cifparse.o
ar: creating cifparse.a
a - lex.cif.o
a - cifp.tab.o
a - cifparse.o
ranlib cifparse.a
mv cifparse.a /home/userid/Documents/amber10/lib
make[1]: Leaving directory `/home/userid/Documents/amber10/src/cifparse'
(cd nab && make install )
make[1]: Entering directory `/home/userid/Documents/amber10/src/nab'
mpicc  -DBINDIR='"."' -DINCDIR='"."' -DLIBDIR='"."'  -m64 -DBINTRAJ -DMPI  \
		-DCC='"mpicc"' -DCPP='"/home/userid/Documents/amber10/bin/ucpp -l"' -DFLIBS='"/home/userid/Documents/amber10/lib/libsym.a /home/userid/Documents/amber10/lib/arpack.a /home/userid/Documents/amber10/lib/lapack.a /home/userid/Documents/amber10/lib/blas.a /home/userid/Documents/amber10/lib/f2c.a    -lmpi"' -o nab nab.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o nab2c.o nab2c.c
flex nablex.l
/home/userid/Documents/amber10/bin/yacc -d nabgrm.y
/home/userid/Documents/amber10/bin/yacc: w - line 332 of "nabgrm.y", the default action assigns an undefined value to $$
/home/userid/Documents/amber10/bin/yacc: 3 shift/reduce conflicts.
mpicc -c -m64 -DBINTRAJ -DMPI  -o cgen.o cgen.c
cgen.c: In function ‘CG_gentype’:
cgen.c:1676: warning: format not a string literal and no format arguments
(cd ../semantics; make)
make[2]: Entering directory `/home/userid/Documents/amber10/src/semantics'
mpicc -DDATDIR='"/home/userid/Documents/amber10/dat"' -o parse parse.c
parse.c: In function ‘fprint_ovalue’:
parse.c:2043: warning: format not a string literal and no format arguments
./parse *.rules
./parse:  82 symbols.
./parse:  19 types, lastuser = 14, v_error = 14.
./parse:   9 classes.
./parse:   8 kinds.
./parse:   4 accesses.
./parse:  27 attributes.
./parse:  40 rules.
./parse:  40 used symbols.
./parse:  15 used types.
./parse:   7 used classes.
./parse:   7 used kinds.
./parse:   0 errors.
make[2]: Leaving directory `/home/userid/Documents/amber10/src/semantics'
mv ../semantics/checkexpr.c .
mpicc -c -m64 -DBINTRAJ -DMPI  -o checkexpr.o checkexpr.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o dumpnode.o dumpnode.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o errormsg.o errormsg.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o fixexpr.o fixexpr.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o genavscode.o genavscode.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o node.o node.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o symbol.o symbol.c
mpicc -c -m64 -DBINTRAJ -DMPI  -Dflex y.tab.c
mpicc  -o nab2c nab2c.o cgen.o checkexpr.o dumpnode.o errormsg.o fixexpr.o genavscode.o node.o symbol.o y.tab.o
./nab  -c  allatom_to_dna3.nab
mpicc -c -m64 -DBINTRAJ -DMPI  -o axis2frame.o axis2frame.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o binpos.o binpos.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  bonded_atoms.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -DDATDIR='"/home/userid/Documents/amber10/dat"' boundsutil.c
boundsutil.c: In function ‘dumpbounds’:
boundsutil.c:888: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
boundsutil.c:892: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
boundsutil.c:893: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
boundsutil.c: In function ‘rd_bmat’:
boundsutil.c:963: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
boundsutil.c:965: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
boundsutil.c:972: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
./nab  -c  lmod.nab
./nab  -c  xmin.nab
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  conjgrad.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o database.o database.c
./nab  -c  dna3.nab
./nab  -c  dna3_to_allatom.nab
mpicc -c -m64 -DBINTRAJ -DMPI  -o dump.o dump.c
flex -t dg_options.l | sed -e 's/yy/dgo/g' -e 's/stdout/nabout/'> lex.dg_options.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -Dflex embed.c
./nab  -c -O0 -DDATDIR='"/home/userid/Documents/amber10/dat"'  fd_helix.nab
mpicc -c -m64 -DBINTRAJ -DMPI  -o frameutil.o frameutil.c
mpicc -c -DDATDIR='"/home/userid/Documents/amber10/dat"'  getdist.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o hashutil.o hashutil.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o jacobi.o jacobi.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  lmodC.c
lmodC.c: In function ‘write_archive’:
lmodC.c:346: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
lmodC.c:347: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
lmodC.c:348: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
lmodC.c:349: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
mpicc -c -m64 -DBINTRAJ -DMPI  -o match.o match.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o matop.o matop.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o memutil.o memutil.c
memutil.c: In function ‘vector’:
memutil.c:31: warning: format ‘%lld’ expects type ‘long long int’, but argument 3 has type ‘size_t’
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  molio.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o molsurf.o molsurf.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o molutil.o molutil.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o dmcsrch.o dmcsrch.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o nab2avs.o nab2avs.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o nab2geom.o nab2geom.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  nblist.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  newton.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o nmode.o nmode.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o chirvol.o chirvol.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o pointutil.o pointutil.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o prm.o prm.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  rand2.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o regexp.o regexp.c
mpicc -c -DDATDIR='"/home/userid/Documents/amber10/dat"'  reslib.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  sasad.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o select_atoms.o select_atoms.c
flex -t mm_options.l | sed -e 's/yy/mmo/g' -e 's/stdout/nabout/' > lex.mm_options.c
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  -Dflex sff.c
In file included from eff.c:1666,
                 from sff.c:795:
gbsa.c: In function ‘egb’:
gbsa.c:177: warning: too few arguments for format
mpicc -c -m64 -DBINTRAJ -DMPI  -o stringutil.o stringutil.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o temputil.o temputil.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o time.o time.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o tm_malloc.o tm_malloc.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o traceback.o traceback.c
traceback.c: In function ‘rt_errormsg’:
traceback.c:14: warning: format not a string literal and no format arguments
./nab  -c  bdna.nab
./nab  -c  dg_helix.nab
./nab  -c  getchivol.nab
./nab  -c  getres.nab
./nab  -c  getseq_from_pdb.nab
./nab  -c  getxyz_from_pdb.nab
./nab  -c -DBINDIR='"/home/userid/Documents/amber10/bin"' -DDATDIR='"/home/userid/Documents/amber10/dat"'  getpdb_prm.nab
./nab  -c  getpdb_rlb.nab
./nab  -c  linkprot.nab
./nab  -c  link_na.nab
./nab  -c -DDATDIR='"/home/userid/Documents/amber10/dat"'  na_anal.nab
na_anal.c: In function ‘local_helical_parameters’:
na_anal.c:795: warning: format not a string literal and no format arguments
na_anal.c:801: warning: format not a string literal and no format arguments
na_anal.c: In function ‘helix_properties’:
na_anal.c:896: warning: format not a string literal and no format arguments
na_anal.c:903: warning: format not a string literal and no format arguments
na_anal.c: In function ‘basepairanal’:
na_anal.c:1800: warning: format not a string literal and no format arguments
./nab  -c  setboundsfromdb.nab
./nab  -c  setchiplane.nab
./nab  -c  wc_basepair.nab
./nab  -c  wc_complement.nab
./nab  -c  wc_helix.nab
mpicc -c -O3 -m64 -DBINTRAJ  -DMPI  xminC.c
./nab  -c  yammp.nab
rm -f libnab.a
ar rv libnab.a allatom_to_dna3.o axis2frame.o binpos.o bonded_atoms.o boundsutil.o lmod.o xmin.o conjgrad.o database.o dna3.o dna3_to_allatom.o dump.o embed.o fd_helix.o frameutil.o getdist.o hashutil.o jacobi.o lmodC.o match.o matop.o memutil.o molio.o molsurf.o molutil.o dmcsrch.o nab2avs.o nab2geom.o nblist.o newton.o nmode.o chirvol.o pointutil.o prm.o rand2.o regexp.o reslib.o sasad.o select_atoms.o sff.o stringutil.o temputil.o time.o tm_malloc.o traceback.o bdna.o dg_helix.o getchivol.o getres.o getseq_from_pdb.o getxyz_from_pdb.o getpdb_prm.o getpdb_rlb.o linkprot.o link_na.o na_anal.o setboundsfromdb.o setchiplane.o wc_basepair.o wc_complement.o wc_helix.o xminC.o yammp.o
ar: creating libnab.a
a - allatom_to_dna3.o
a - axis2frame.o
a - binpos.o
a - bonded_atoms.o
a - boundsutil.o
a - lmod.o
a - xmin.o
a - conjgrad.o
a - database.o
a - dna3.o
a - dna3_to_allatom.o
a - dump.o
a - embed.o
a - fd_helix.o
a - frameutil.o
a - getdist.o
a - hashutil.o
a - jacobi.o
a - lmodC.o
a - match.o
a - matop.o
a - memutil.o
a - molio.o
a - molsurf.o
a - molutil.o
a - dmcsrch.o
a - nab2avs.o
a - nab2geom.o
a - nblist.o
a - newton.o
a - nmode.o
a - chirvol.o
a - pointutil.o
a - prm.o
a - rand2.o
a - regexp.o
a - reslib.o
a - sasad.o
a - select_atoms.o
a - sff.o
a - stringutil.o
a - temputil.o
a - time.o
a - tm_malloc.o
a - traceback.o
a - bdna.o
a - dg_helix.o
a - getchivol.o
a - getres.o
a - getseq_from_pdb.o
a - getxyz_from_pdb.o
a - getpdb_prm.o
a - getpdb_rlb.o
a - linkprot.o
a - link_na.o
a - na_anal.o
a - setboundsfromdb.o
a - setchiplane.o
a - wc_basepair.o
a - wc_complement.o
a - wc_helix.o
a - xminC.o
a - yammp.o
ranlib libnab.a
mpicc -DBINDIR='"/home/userid/Documents/amber10/bin"' \
		-DINCDIR='"/home/userid/Documents/amber10/include"' \
		-DLIBDIR='"/home/userid/Documents/amber10/lib"' \
		-m64 -DBINTRAJ -DMPI  -DCC='"mpicc"' -DCPP='"/home/userid/Documents/amber10/bin/ucpp -l"' -DFLIBS='"/home/userid/Documents/amber10/lib/libsym.a /home/userid/Documents/amber10/lib/arpack.a /home/userid/Documents/amber10/lib/lapack.a /home/userid/Documents/amber10/lib/blas.a /home/userid/Documents/amber10/lib/f2c.a    -lmpi"' \
		-o nab_install nab.c
mkdir /home/userid/Documents/amber10/lib /home/userid/Documents/amber10/bin /home/userid/Documents/amber10/include
mkdir: cannot create directory `/home/userid/Documents/amber10/lib': File exists
mkdir: cannot create directory `/home/userid/Documents/amber10/bin': File exists
mkdir: cannot create directory `/home/userid/Documents/amber10/include': File exists
make[1]: [install] Error 1 (ignored)
mv -f  nab_install /home/userid/Documents/amber10/bin/nab
mv -f  nab2c /home/userid/Documents/amber10/bin
mv -f  libnab.a /home/userid/Documents/amber10/lib
rm -f /home/userid/Documents/amber10/include/nabcode.h /home/userid/Documents/amber10/include/defreal.h /home/userid/Documents/amber10/include/nab.h
cp nabcode.h /home/userid/Documents/amber10/include
cp nabtypes.h /home/userid/Documents/amber10/include
cp defreal.h /home/userid/Documents/amber10/include
cp nab.h /home/userid/Documents/amber10/include
cp xmin_opt.h lmod_opt.h /home/userid/Documents/amber10/include
cp lmodprmtop /home/userid/Documents/amber10/bin
make[1]: Leaving directory `/home/userid/Documents/amber10/src/nab'
(cd nss && make install )
make[1]: Entering directory `/home/userid/Documents/amber10/src/nss'
Makefile:17: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
/home/userid/Documents/amber10/bin/nab -c symop.nab
symop.c: In function ‘MAT_ico’:
symop.c:219: warning: passing argument 2 of ‘rot4p’ from incompatible pointer type
/home/userid/Documents/amber10/bin/nab -c matop.c
/home/userid/Documents/amber10/bin/nab -c tss.c
ar rv libsym.a symop.o matop.o tss.o
ar: creating libsym.a
a - symop.o
a - matop.o
a - tss.o
ranlib libsym.a
cp -p libsym.a /home/userid/Documents/amber10/lib
/home/userid/Documents/amber10/bin/nab -c matextract.nab
/home/userid/Documents/amber10/bin/nab -o matextract matextract.o libsym.a
/home/userid/Documents/amber10/bin/nab -c matgen.nab
/home/userid/Documents/amber10/bin/nab -o matgen matgen.o libsym.a
/home/userid/Documents/amber10/bin/nab -c matmerge.nab
/home/userid/Documents/amber10/bin/nab -o matmerge matmerge.o libsym.a
/home/userid/Documents/amber10/bin/nab -c matmul.nab
/home/userid/Documents/amber10/bin/nab -o matmul matmul.o libsym.a
/home/userid/Documents/amber10/bin/nab -c transform.nab
transform.c: In function ‘main’:
transform.c:82: warning: passing argument 3 of ‘setxyz_from_mol’ from incompatible pointer type
transform.c:85: warning: passing argument 3 of ‘setmol_from_xyz’ from incompatible pointer type
transform.c:121: warning: passing argument 2 of ‘transformpts’ from incompatible pointer type
/home/userid/Documents/amber10/bin/nab -o transform transform.o libsym.a
/home/userid/Documents/amber10/bin/nab -c tss_init.nab
/home/userid/Documents/amber10/bin/nab -o tss_init tss_init.o libsym.a
/home/userid/Documents/amber10/bin/nab -c tss_main.nab
tss_main.c: In function ‘main’:
tss_main.c:306: warning: passing argument 3 of ‘setxyz_from_mol’ from incompatible pointer type
tss_main.c:307: warning: passing argument 2 of ‘transformpts’ from incompatible pointer type
tss_main.c:308: warning: passing argument 3 of ‘setmol_from_xyz’ from incompatible pointer type
/home/userid/Documents/amber10/bin/nab -o tss_main tss_main.o libsym.a
tss_main.o: In function `main':
tss_main.c:(.text+0xa97): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
/home/userid/Documents/amber10/bin/nab -c tss_next.nab
/home/userid/Documents/amber10/bin/nab -o tss_next tss_next.o libsym.a
cp -p matextract matgen matmerge matmul \
		transform tss_init tss_main \
		tss_next /home/userid/Documents/amber10/bin
cp -p libsym.a /home/userid/Documents/amber10/lib
make[1]: Leaving directory `/home/userid/Documents/amber10/src/nss'
(cd antechamber && make install )
make[1]: Entering directory `/home/userid/Documents/amber10/src/antechamber'
Makefile:219: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
mpicc -m64 -DBINTRAJ -DMPI  -c -DDATDIR='"/home/userid/Documents/amber10/dat"' -DBINDIR='"/home/userid/Documents/amber10/bin"' am1bcc.c
mpicc  am1bcc.o -lm -o am1bcc  
mpicc -m64 -DBINTRAJ -DMPI  -c -DDATDIR='"/home/userid/Documents/amber10/dat"' -DBINDIR='"/home/userid/Documents/amber10/bin"' acdoctor.c
mpicc  acdoctor.o -lm -o acdoctor  
mpicc -m64 -DBINTRAJ -DMPI  -c -DDATDIR='"/home/userid/Documents/amber10/dat"' -DBINDIR='"/home/userid/Documents/amber10/bin"' antechamber.c
mpicc  antechamber.o -lm -o antechamber  
mpicc -m64 -DBINTRAJ -DMPI  -c -DDATDIR='"/home/userid/Documents/amber10/dat"' -DBINDIR='"/home/userid/Documents/amber10/bin"' atomtype.c
mpicc  atomtype.o -lm -o atomtype  
mpicc -m64 -DBINTRAJ -DMPI  -c -DDATDIR='"/home/userid/Documents/amber10/dat"' -DBINDIR='"/home/userid/Documents/amber10/bin"' bondtype.c
mpicc -m64 -DBINTRAJ -DMPI  -c -DDATDIR='"/home/userid/Documents/amber10/dat"' -DBINDIR='"/home/userid/Documents/amber10/bin"' ncsu-penalties.c
mpicc  ncsu-penalties.o bondtype.o -o bondtype  
mpicc -m64 -DBINTRAJ -DMPI  -c -DDATDIR='"/home/userid/Documents/amber10/dat"' -DBINDIR='"/home/userid/Documents/amber10/bin"' charmmgen.c
mpicc  charmmgen.o -lm -o charmmgen
mpicc -m64 -DBINTRAJ -DMPI  -c -DDATDIR='"/home/userid/Documents/amber10/dat"' -DBINDIR='"/home/userid/Documents/amber10/bin"' database.c
mpicc  database.o -lm -o database
mpicc -m64 -DBINTRAJ -DMPI  -c -DDATDIR='"/home/userid/Documents/amber10/dat"' -DBINDIR='"/home/userid/Documents/amber10/bin"' espgen.c
mpicc  espgen.o -o espgen
mpicc -m64 -DBINTRAJ -DMPI  -c -DDATDIR='"/home/userid/Documents/amber10/dat"' -DBINDIR='"/home/userid/Documents/amber10/bin"' parmcal.c
mpicc  parmcal.o -lm -o parmcal
mpicc -m64 -DBINTRAJ -DMPI  -c -DDATDIR='"/home/userid/Documents/amber10/dat"' -DBINDIR='"/home/userid/Documents/amber10/bin"' parmchk.c
mpicc  parmchk.o -lm -o parmchk
mpicc -m64 -DBINTRAJ -DMPI  -c -DDATDIR='"/home/userid/Documents/amber10/dat"' -DBINDIR='"/home/userid/Documents/amber10/bin"' prepgen.c
mpicc  prepgen.o -lm -o prepgen
mpicc -m64 -DBINTRAJ -DMPI  -c -DDATDIR='"/home/userid/Documents/amber10/dat"' -DBINDIR='"/home/userid/Documents/amber10/bin"' residuegen.c
mpicc  residuegen.o -lm -o residuegen
mpicc -m64 -DBINTRAJ -DMPI  -c -DDATDIR='"/home/userid/Documents/amber10/dat"' -DBINDIR='"/home/userid/Documents/amber10/bin"' respgen.c
mpicc  respgen.o -lm -o respgen
mpicc -m64 -DBINTRAJ -DMPI  -c -DDATDIR='"/home/userid/Documents/amber10/dat"' -DBINDIR='"/home/userid/Documents/amber10/bin"' translate.c
mpicc  translate.o -lm -o translate
mpicc -m64 -DBINTRAJ -DMPI  -c -DDATDIR='"/home/userid/Documents/amber10/dat"' -DBINDIR='"/home/userid/Documents/amber10/bin"' top2mol2.c
mpicc  top2mol2.o -lm -o top2mol2
sed -e "s?BINDIR?/home/userid/Documents/amber10/bin?" mopac.sh > /home/userid/Documents/amber10/bin/mopac.sh
chmod +x /home/userid/Documents/amber10/bin/mopac.sh
mv -f am1bcc acdoctor antechamber atomtype bondtype charmmgen database espgen parmcal parmchk prepgen residuegen respgen translate top2mol2 /home/userid/Documents/amber10/bin
make[1]: Leaving directory `/home/userid/Documents/amber10/src/antechamber'
(cd mopac6/src && make hasG77 )
make[1]: Entering directory `/home/userid/Documents/amber10/src/mopac6/src'
gfortran -c -O1 -fno-automatic   -o aababc.o aababc.f
gfortran -c -O1 -fno-automatic   -o readmo.o readmo.f
gfortran -c -O1 -fno-automatic   -o writmo.o writmo.f
gfortran -c -O1 -fno-automatic   -o mopac.o mopac.f
gfortran -c -O1 -fno-automatic   -o analyt.o analyt.f
gfortran -c -O1 -fno-automatic   -o anavib.o anavib.f
gfortran -c -O1 -fno-automatic   -o axis.o axis.f
gfortran -c -O1 -fno-automatic   -o block.o block.f
gfortran -c -O1 -fno-automatic   -o bonds.o bonds.f
gfortran -c -O1 -fno-automatic   -o brlzon.o brlzon.f
gfortran -c -O1 -fno-automatic   -o calpar.o calpar.f
gfortran -c -O1 -fno-automatic   -o capcor.o capcor.f
gfortran -c -O1 -fno-automatic   -o cdiag.o cdiag.f
gfortran -c -O1 -fno-automatic   -o chrge.o chrge.f
gfortran -c -O1 -fno-automatic   -o cnvg.o cnvg.f
gfortran -c -O1 -fno-automatic   -o compfg.o compfg.f
gfortran -c -O1 -fno-automatic   -o datin.o datin.f
gfortran -c -O1 -fno-automatic   -o dcart.o dcart.f
gfortran -c -O1 -fno-automatic   -o delmol.o delmol.f
gfortran -c -O1 -fno-automatic   -o delri.o delri.f
gfortran -c -O1 -fno-automatic   -o denrot.o denrot.f
gfortran -c -O1 -fno-automatic   -o densit.o densit.f
gfortran -c -O1 -fno-automatic   -o depvar.o depvar.f
gfortran -c -O1 -fno-automatic   -o deri0.o deri0.f
gfortran -c -O1 -fno-automatic   -o deri1.o deri1.f
gfortran -c -O1 -fno-automatic   -o deri2.o deri2.f
gfortran -c -O1 -fno-automatic   -o deri21.o deri21.f
gfortran -c -O1 -fno-automatic   -o deri22.o deri22.f
gfortran -c -O1 -fno-automatic   -o deri23.o deri23.f
gfortran -c -O1 -fno-automatic   -o deritr.o deritr.f
gfortran -c -O1 -fno-automatic   -o deriv.o deriv.f
gfortran -c -O1 -fno-automatic   -o dernvo.o dernvo.f
gfortran -c -O1 -fno-automatic   -o ders.o ders.f
gfortran -c -O1 -fno-automatic   -o dfock2.o dfock2.f
gfortran -c -O1 -fno-automatic   -o dfpsav.o dfpsav.f
gfortran -c -O1 -fno-automatic   -o diag.o diag.f
gfortran -c -O1 -fno-automatic   -o diat.o diat.f
gfortran -c -O1 -fno-automatic   -o diat2.o diat2.f
gfortran -c -O1 -fno-automatic   -o diis.o diis.f
gfortran -c -O1 -fno-automatic   -o dijkl1.o dijkl1.f
gfortran -c -O1 -fno-automatic   -o dijkl2.o dijkl2.f
gfortran -c -O1 -fno-automatic   -o dipind.o dipind.f
gfortran -c -O1 -fno-automatic   -o dipole.o dipole.f
gfortran -c -O1 -fno-automatic   -o dofs.o dofs.f
gfortran -c -O1 -fno-automatic   -o dot.o dot.f
gfortran -c -O1 -fno-automatic   -o drc.o drc.f
gfortran -c -O1 -fno-automatic   -o drcout.o drcout.f
gfortran -c -O1 -fno-automatic   -o ef.o ef.f
gfortran -c -O1 -fno-automatic   -o enpart.o enpart.f
gfortran -c -O1 -fno-automatic   -o exchng.o exchng.f
gfortran -c -O1 -fno-automatic   -o ffhpol.o ffhpol.f
gfortran -c -O1 -fno-automatic   -o flepo.o flepo.f
gfortran -c -O1 -fno-automatic   -o fmat.o fmat.f
gfortran -c -O1 -fno-automatic   -o fock1.o fock1.f
gfortran -c -O1 -fno-automatic   -o fock2.o fock2.f
gfortran -c -O1 -fno-automatic   -o force.o force.f
gfortran -c -O1 -fno-automatic   -o formxy.o formxy.f
gfortran -c -O1 -fno-automatic   -o forsav.o forsav.f
gfortran -c -O1 -fno-automatic   -o frame.o frame.f
gfortran -c -O1 -fno-automatic   -o freqcy.o freqcy.f
gfortran -c -O1 -fno-automatic   -o geout.o geout.f
gfortran -c -O1 -fno-automatic   -o geoutg.o geoutg.f
gfortran -c -O1 -fno-automatic   -o getgeg.o getgeg.f
gfortran -c -O1 -fno-automatic   -o getgeo.o getgeo.f
gfortran -c -O1 -fno-automatic   -o getsym.o getsym.f
gfortran -c -O1 -fno-automatic   -o gettxt.o gettxt.f
gfortran -c -O1 -fno-automatic   -o gmetry.o gmetry.f
gfortran -c -O1 -fno-automatic   -o gover.o gover.f
gfortran -c -O1 -fno-automatic   -o grid.o grid.f
gfortran -c -O1 -fno-automatic   -o h1elec.o h1elec.f
gfortran -c -O1 -fno-automatic   -o haddon.o haddon.f
gfortran -c -O1 -fno-automatic   -o hcore.o hcore.f
gfortran -c -O1 -fno-automatic   -o helect.o helect.f
gfortran -c -O1 -fno-automatic   -o hqrii.o hqrii.f
gfortran -c -O1 -fno-automatic   -o ijkl.o ijkl.f
gfortran -c -O1 -fno-automatic   -o interp.o interp.f
gfortran -c -O1 -fno-automatic   -o iter.o iter.f
gfortran -c -O1 -fno-automatic   -o jcarin.o jcarin.f
gfortran -c -O1 -fno-automatic   -o linmin.o linmin.f
gfortran -c -O1 -fno-automatic   -o local.o local.f
gfortran -c -O1 -fno-automatic   -o locmin.o locmin.f
gfortran -c -O1 -fno-automatic   -o mamult.o mamult.f
gfortran -c -O1 -fno-automatic   -o matout.o matout.f
gfortran -c -O1 -fno-automatic   -o matpak.o matpak.f
gfortran -c -O1 -fno-automatic   -o meci.o meci.f
gfortran -c -O1 -fno-automatic   -o mecid.o mecid.f
gfortran -c -O1 -fno-automatic   -o mecih.o mecih.f
gfortran -c -O1 -fno-automatic   -o mecip.o mecip.f
gfortran -c -O1 -fno-automatic   -o moldat.o moldat.f
gfortran -c -O1 -fno-automatic   -o molval.o molval.f
gfortran -c -O1 -fno-automatic   -o mullik.o mullik.f
gfortran -c -O1 -fno-automatic   -o mult.o mult.f
gfortran -c -O1 -fno-automatic   -o nllsq.o nllsq.f
gfortran -c -O1 -fno-automatic   -o nuchar.o nuchar.f
gfortran -c -O1 -fno-automatic   -o parsav.o parsav.f
gfortran -c -O1 -fno-automatic   -o partxy.o partxy.f
gfortran -c -O1 -fno-automatic   -o pathk.o pathk.f
gfortran -c -O1 -fno-automatic   -o paths.o paths.f
gfortran -c -O1 -fno-automatic   -o perm.o perm.f
gfortran -c -O1 -fno-automatic   -o polar.o polar.f
gfortran -c -O1 -fno-automatic   -o powsav.o powsav.f
gfortran -c -O1 -fno-automatic   -o powsq.o powsq.f
gfortran -c -O1 -fno-automatic   -o prtdrc.o prtdrc.f
gfortran -c -O1 -fno-automatic   -o quadr.o quadr.f
gfortran -c -O1 -fno-automatic   -o react1.o react1.f
gfortran -c -O1 -fno-automatic   -o reada.o reada.f
gfortran -c -O1 -fno-automatic   -o refer.o refer.f
gfortran -c -O1 -fno-automatic   -o repp.o repp.f
gfortran -c -O1 -fno-automatic   -o rotat.o rotat.f
gfortran -c -O1 -fno-automatic   -o rotate.o rotate.f
gfortran -c -O1 -fno-automatic   -o rsp.o rsp.f
gfortran -c -O1 -fno-automatic   -o search.o search.f
gfortran -c -O1 -fno-automatic   -o second.o second.f
gfortran -c -O1 -fno-automatic   -o setupg.o setupg.f
gfortran -c -O1 -fno-automatic   -o solrot.o solrot.f
gfortran -c -O1 -fno-automatic   -o swap.o swap.f
gfortran -c -O1 -fno-automatic   -o symtry.o symtry.f
gfortran -c -O1 -fno-automatic   -o thermo.o thermo.f
gfortran -c -O1 -fno-automatic   -o timer.o timer.f
gfortran -c -O1 -fno-automatic   -o update.o update.f
gfortran -c -O1 -fno-automatic   -o vecprt.o vecprt.f
gfortran -c -O1 -fno-automatic   -o wrtkey.o wrtkey.f
gfortran -c -O1 -fno-automatic   -o wrttxt.o wrttxt.f
gfortran -c -O1 -fno-automatic   -o xyzint.o xyzint.f
gfortran  aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o   -o mopac
mv mopac /home/userid/Documents/amber10/bin
make[1]: Leaving directory `/home/userid/Documents/amber10/src/mopac6/src'
(cd resp && make hasG77 )
make[1]: Entering directory `/home/userid/Documents/amber10/src/resp'
gfortran -c -O1 -fno-automatic   -o lapack.o lapack.f
gfortran -c -O1 -fno-automatic   -o resp.o resp.f
gfortran   lapack.o resp.o   -o resp
mv resp /home/userid/Documents/amber10/bin
make[1]: Leaving directory `/home/userid/Documents/amber10/src/resp'
(cd ptraj && make install )
make[1]: Entering directory `/home/userid/Documents/amber10/src/ptraj'
Makefile:24: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
cd pdb; make 
make[2]: Entering directory `/home/userid/Documents/amber10/src/ptraj/pdb'
mpicc -c -m64 -DBINTRAJ -DMPI  -o pdbrun.o pdbrun.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o pdb_read.o pdb_read.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o pdb_sprntf.o pdb_sprntf.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o pdb_sscanf.o pdb_sscanf.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o pdb_write.o pdb_write.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o ms.o ms.c
ar rv libpdb.a pdbrun.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o ms.o
ar: creating libpdb.a
a - pdbrun.o
a - pdb_read.o
a - pdb_sprntf.o
a - pdb_sscanf.o
a - pdb_write.o
a - ms.o
ranlib libpdb.a
mv libpdb.a /home/userid/Documents/amber10/lib
make[2]: Leaving directory `/home/userid/Documents/amber10/src/ptraj/pdb'
cd ../netcdf/src; make install
make[2]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src'
Making install in libsrc
make[3]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/libsrc'
depbase=`echo attr.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
	if /bin/bash ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran      -m64 -DBINTRAJ -MT attr.lo -MD -MP -MF "$depbase.Tpo" -c -o attr.lo attr.c; \
	then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
 mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT attr.lo -MD -MP -MF .deps/attr.Tpo -c attr.c -o attr.o
depbase=`echo ncx.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
	if /bin/bash ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran      -m64 -DBINTRAJ -MT ncx.lo -MD -MP -MF "$depbase.Tpo" -c -o ncx.lo ncx.c; \
	then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
 mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT ncx.lo -MD -MP -MF .deps/ncx.Tpo -c ncx.c -o ncx.o
depbase=`echo putget.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
	if /bin/bash ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran      -m64 -DBINTRAJ -MT putget.lo -MD -MP -MF "$depbase.Tpo" -c -o putget.lo putget.c; \
	then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
 mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT putget.lo -MD -MP -MF .deps/putget.Tpo -c putget.c -o putget.o
depbase=`echo dim.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
	if /bin/bash ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran      -m64 -DBINTRAJ -MT dim.lo -MD -MP -MF "$depbase.Tpo" -c -o dim.lo dim.c; \
	then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
 mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT dim.lo -MD -MP -MF .deps/dim.Tpo -c dim.c -o dim.o
depbase=`echo error.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
	if /bin/bash ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran      -m64 -DBINTRAJ -MT error.lo -MD -MP -MF "$depbase.Tpo" -c -o error.lo error.c; \
	then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
 mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT error.lo -MD -MP -MF .deps/error.Tpo -c error.c -o error.o
depbase=`echo libvers.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
	if /bin/bash ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran      -m64 -DBINTRAJ -MT libvers.lo -MD -MP -MF "$depbase.Tpo" -c -o libvers.lo libvers.c; \
	then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
 mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT libvers.lo -MD -MP -MF .deps/libvers.Tpo -c libvers.c -o libvers.o
depbase=`echo nc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
	if /bin/bash ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran      -m64 -DBINTRAJ -MT nc.lo -MD -MP -MF "$depbase.Tpo" -c -o nc.lo nc.c; \
	then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
 mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT nc.lo -MD -MP -MF .deps/nc.Tpo -c nc.c -o nc.o
depbase=`echo string.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
	if /bin/bash ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran      -m64 -DBINTRAJ -MT string.lo -MD -MP -MF "$depbase.Tpo" -c -o string.lo string.c; \
	then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
 mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT string.lo -MD -MP -MF .deps/string.Tpo -c string.c -o string.o
depbase=`echo v1hpg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
	if /bin/bash ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran      -m64 -DBINTRAJ -MT v1hpg.lo -MD -MP -MF "$depbase.Tpo" -c -o v1hpg.lo v1hpg.c; \
	then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
 mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT v1hpg.lo -MD -MP -MF .deps/v1hpg.Tpo -c v1hpg.c -o v1hpg.o
depbase=`echo var.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
	if /bin/bash ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran      -m64 -DBINTRAJ -MT var.lo -MD -MP -MF "$depbase.Tpo" -c -o var.lo var.c; \
	then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
 mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT var.lo -MD -MP -MF .deps/var.Tpo -c var.c -o var.o
depbase=`echo posixio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
	if /bin/bash ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran      -m64 -DBINTRAJ -MT posixio.lo -MD -MP -MF "$depbase.Tpo" -c -o posixio.lo posixio.c; \
	then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
 mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT posixio.lo -MD -MP -MF .deps/posixio.Tpo -c posixio.c -o posixio.o
depbase=`echo v2i.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
	if /bin/bash ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran      -m64 -DBINTRAJ -MT v2i.lo -MD -MP -MF "$depbase.Tpo" -c -o v2i.lo v2i.c; \
	then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
 mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -m64 -DBINTRAJ -MT v2i.lo -MD -MP -MF .deps/v2i.Tpo -c v2i.c -o v2i.o
/bin/bash ../libtool --tag=CC --mode=link mpicc  -m64 -DBINTRAJ   -o libnetcdf2.la   v2i.lo  
mkdir .libs
ar cru .libs/libnetcdf2.a  v2i.o
ranlib .libs/libnetcdf2.a
creating libnetcdf2.la
(cd .libs && rm -f libnetcdf2.la && ln -s ../libnetcdf2.la libnetcdf2.la)
/bin/bash ../libtool --tag=CC --mode=link mpicc  -m64 -DBINTRAJ   -o libnetcdf.la -rpath /home/userid/Documents/amber10/src/netcdf/lib  -version-info 4:0:0 -no-undefined  attr.lo ncx.lo putget.lo dim.lo error.lo libvers.lo nc.lo string.lo v1hpg.lo var.lo  posixio.lo libnetcdf2.la  
rm -fr .libs/libnetcdf.lax
mkdir .libs/libnetcdf.lax
rm -fr .libs/libnetcdf.lax/libnetcdf2.a
mkdir .libs/libnetcdf.lax/libnetcdf2.a
(cd .libs/libnetcdf.lax/libnetcdf2.a && ar x /home/userid/Documents/amber10/src/netcdf/src/libsrc/./.libs/libnetcdf2.a)
ar cru .libs/libnetcdf.a  attr.o ncx.o putget.o dim.o error.o libvers.o nc.o string.o v1hpg.o var.o posixio.o  .libs/libnetcdf.lax/libnetcdf2.a/v2i.o 
ranlib .libs/libnetcdf.a
rm -fr .libs/libnetcdf.lax
creating libnetcdf.la
(cd .libs && rm -f libnetcdf.la && ln -s ../libnetcdf.la libnetcdf.la)
make[4]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/libsrc'
test -z "/home/userid/Documents/amber10/src/netcdf/lib" || mkdir -p -- "/home/userid/Documents/amber10/src/netcdf/lib"
 /bin/bash ../libtool --mode=install /usr/bin/install -c  'libnetcdf.la' '/home/userid/Documents/amber10/src/netcdf/lib/libnetcdf.la'
/usr/bin/install -c .libs/libnetcdf.lai /home/userid/Documents/amber10/src/netcdf/lib/libnetcdf.la
/usr/bin/install -c .libs/libnetcdf.a /home/userid/Documents/amber10/src/netcdf/lib/libnetcdf.a
chmod 644 /home/userid/Documents/amber10/src/netcdf/lib/libnetcdf.a
ranlib /home/userid/Documents/amber10/src/netcdf/lib/libnetcdf.a
PATH="$PATH:/sbin" ldconfig -n /home/userid/Documents/amber10/src/netcdf/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/userid/Documents/amber10/src/netcdf/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,--rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
test -z "/home/userid/Documents/amber10/src/netcdf/include" || mkdir -p -- "/home/userid/Documents/amber10/src/netcdf/include"
 /usr/bin/install -c -m 644 'netcdf.h' '/home/userid/Documents/amber10/src/netcdf/include/netcdf.h'
test -z "/home/userid/Documents/amber10/src/netcdf/share/man/man3" || mkdir -p -- "/home/userid/Documents/amber10/src/netcdf/share/man/man3"
 /usr/bin/install -c -m 644 './netcdf.3' '/home/userid/Documents/amber10/src/netcdf/share/man/man3/netcdf.3'
make[4]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/libsrc'
make[3]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/libsrc'
Making install in nctest
make[3]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/nctest'
make[4]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/nctest'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/nctest'
make[3]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/nctest'
Making install in ncgen
make[3]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/ncgen'
depbase=`echo main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
	if mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran  -I.. -I../libsrc -I../libsrc   -m64 -DBINTRAJ -MT main.o -MD -MP -MF "$depbase.Tpo" -c -o main.o main.c; \
	then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo load.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
	if mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran  -I.. -I../libsrc -I../libsrc   -m64 -DBINTRAJ -MT load.o -MD -MP -MF "$depbase.Tpo" -c -o load.o load.c; \
	then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo ncgentab.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
	if mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran  -I.. -I../libsrc -I../libsrc   -m64 -DBINTRAJ -MT ncgentab.o -MD -MP -MF "$depbase.Tpo" -c -o ncgentab.o ncgentab.c; \
	then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo escapes.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
	if mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran  -I.. -I../libsrc -I../libsrc   -m64 -DBINTRAJ -MT escapes.o -MD -MP -MF "$depbase.Tpo" -c -o escapes.o escapes.c; \
	then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo getfill.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
	if mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran  -I.. -I../libsrc -I../libsrc   -m64 -DBINTRAJ -MT getfill.o -MD -MP -MF "$depbase.Tpo" -c -o getfill.o getfill.c; \
	then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo init.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
	if mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran  -I.. -I../libsrc -I../libsrc   -m64 -DBINTRAJ -MT init.o -MD -MP -MF "$depbase.Tpo" -c -o init.o init.c; \
	then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo genlib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
	if mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran  -I.. -I../libsrc -I../libsrc   -m64 -DBINTRAJ -MT genlib.o -MD -MP -MF "$depbase.Tpo" -c -o genlib.o genlib.c; \
	then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
/bin/bash ../libtool --tag=CC --mode=link mpicc  -m64 -DBINTRAJ   -o ncgen  main.o load.o ncgentab.o escapes.o getfill.o init.o genlib.o ../libsrc/libnetcdf.la 
mkdir .libs
mpicc -m64 -DBINTRAJ -o ncgen main.o load.o ncgentab.o escapes.o getfill.o init.o genlib.o  ../libsrc/.libs/libnetcdf.a  
make[4]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/ncgen'
test -z "/home/userid/Documents/amber10/src/netcdf/bin" || mkdir -p -- "/home/userid/Documents/amber10/src/netcdf/bin"
  /bin/bash ../libtool --mode=install /usr/bin/install -c 'ncgen' '/home/userid/Documents/amber10/src/netcdf/bin/ncgen'
/usr/bin/install -c ncgen /home/userid/Documents/amber10/src/netcdf/bin/ncgen
test -z "/home/userid/Documents/amber10/src/netcdf/share/man/man1" || mkdir -p -- "/home/userid/Documents/amber10/src/netcdf/share/man/man1"
 /usr/bin/install -c -m 644 './ncgen.1' '/home/userid/Documents/amber10/src/netcdf/share/man/man1/ncgen.1'
make[4]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/ncgen'
make[3]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/ncgen'
Making install in ncdump
make[3]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/ncdump'
depbase=`echo ncdump.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
	if mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran  -I../libsrc -I../libsrc   -m64 -DBINTRAJ -MT ncdump.o -MD -MP -MF "$depbase.Tpo" -c -o ncdump.o ncdump.c; \
	then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo vardata.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
	if mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran  -I../libsrc -I../libsrc   -m64 -DBINTRAJ -MT vardata.o -MD -MP -MF "$depbase.Tpo" -c -o vardata.o vardata.c; \
	then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
vardata.c: In function ‘pr_bvals’:
vardata.c:491: warning: format not a string literal and no format arguments
vardata.c:501: warning: format not a string literal and no format arguments
vardata.c: In function ‘pr_svals’:
vardata.c:539: warning: format not a string literal and no format arguments
vardata.c:549: warning: format not a string literal and no format arguments
vardata.c: In function ‘pr_ivals’:
vardata.c:589: warning: format not a string literal and no format arguments
vardata.c:599: warning: format not a string literal and no format arguments
vardata.c: In function ‘pr_fvals’:
vardata.c:637: warning: format not a string literal and no format arguments
vardata.c:647: warning: format not a string literal and no format arguments
vardata.c: In function ‘pr_dvals’:
vardata.c:685: warning: format not a string literal and no format arguments
vardata.c:695: warning: format not a string literal and no format arguments
depbase=`echo dumplib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
	if mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran  -I../libsrc -I../libsrc   -m64 -DBINTRAJ -MT dumplib.o -MD -MP -MF "$depbase.Tpo" -c -o dumplib.o dumplib.c; \
	then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
/bin/bash ../libtool --tag=CC --mode=link mpicc  -m64 -DBINTRAJ   -o ncdump  ncdump.o vardata.o dumplib.o -lm  ../libsrc/libnetcdf.la 
mkdir .libs
mpicc -m64 -DBINTRAJ -o ncdump ncdump.o vardata.o dumplib.o  -lm ../libsrc/.libs/libnetcdf.a  
make[4]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/ncdump'
test -z "/home/userid/Documents/amber10/src/netcdf/bin" || mkdir -p -- "/home/userid/Documents/amber10/src/netcdf/bin"
  /bin/bash ../libtool --mode=install /usr/bin/install -c 'ncdump' '/home/userid/Documents/amber10/src/netcdf/bin/ncdump'
/usr/bin/install -c ncdump /home/userid/Documents/amber10/src/netcdf/bin/ncdump
test -z "/home/userid/Documents/amber10/src/netcdf/share/man/man1" || mkdir -p -- "/home/userid/Documents/amber10/src/netcdf/share/man/man1"
 /usr/bin/install -c -m 644 './ncdump.1' '/home/userid/Documents/amber10/src/netcdf/share/man/man1/ncdump.1'
make[4]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/ncdump'
make[3]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/ncdump'
Making install in nc_test
make[3]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/nc_test'
make[4]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/nc_test'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/nc_test'
make[3]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/nc_test'
Making install in examples
make[3]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/examples'
Making install in C
make[4]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/examples/C'
make[5]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/examples/C'
make[5]: Nothing to be done for `install-exec-am'.
make[5]: Nothing to be done for `install-data-am'.
make[5]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/examples/C'
make[4]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/examples/C'
Making install in CDL
make[4]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/examples/CDL'
make[5]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/examples/CDL'
make[5]: Nothing to be done for `install-exec-am'.
make[5]: Nothing to be done for `install-data-am'.
make[5]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/examples/CDL'
make[4]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/examples/CDL'
make[4]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/examples'
make[5]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src/examples'
make[5]: Nothing to be done for `install-exec-am'.
make[5]: Nothing to be done for `install-data-am'.
make[5]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/examples'
make[4]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/examples'
make[3]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src/examples'
make[3]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src'
make[4]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src'
make[4]: Nothing to be done for `install-exec-am'.
make  install-data-hook
make[5]: Entering directory `/home/userid/Documents/amber10/src/netcdf/src'

+-------------------------------------------------------------+
| CAUTION:                                                    |
|                                                             |
| If you have not already run "make check", then we strongly  |
| recommend you do so. It does not take very long.            |
|                                                             |
| Before using netCDF to store important data, test your      |
| build with "make check".                                    |
|                                                             |
| NetCDF is tested nightly on many platforms at Unidata       |
| but your platform is probably different in some ways.       |
|                                                             |
| If any tests fail, please see the netCDF web site:          |
| http://www.unidata.ucar.edu/software/netcdf/                |
|                                                             |
| NetCDF is developed and maintained at the Unidata Program   |
| Center. Unidata provides a broad array of data and software |
| tools for use in geoscience education and research.         |
| http://www.unidata.ucar.edu                                 |
+-------------------------------------------------------------+

make[5]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src'
make[4]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src'
make[3]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src'
make[2]: Leaving directory `/home/userid/Documents/amber10/src/netcdf/src'
mpicc -c -m64 -DBINTRAJ -DMPI   -o main.o main.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o rdparm.o rdparm.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o dispatch.o dispatch.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o help.o help.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o utility.o utility.c
utility.c: In function ‘SafeMalloc’:
utility.c:162: warning: format ‘%i’ expects type ‘int’, but argument 5 has type ‘size_t’
mpicc -c -m64 -DBINTRAJ -DMPI   -o second.o second.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o io.o io.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o trajectory.o trajectory.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o evec.o evec.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o torsion.o torsion.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o mask.o mask.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o rms.o rms.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o display.o display.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o interface.o interface.c
interface.c: In function ‘interface’:
interface.c:100: warning: format not a string literal and no format arguments
interface.c:101: warning: format not a string literal and no format arguments
interface.c:115: warning: format not a string literal and no format arguments
mpicc -c -m64 -DBINTRAJ -DMPI   -o energy.o energy.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o experimental.o experimental.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o ptraj.o ptraj.c
ptraj.c: In function ‘checkCoordinates’:
ptraj.c:2147: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘pdb_record’
ptraj.c: In function ‘loadCharmmPSF’:
ptraj.c:2834: warning: format ‘%4s’ expects type ‘char *’, but argument 5 has type ‘char (*)[5]’
mpicc -c -m64 -DBINTRAJ -DMPI   -o actions.o actions.c
actions.c: In function ‘transformCluster’:
actions.c:3603: warning: format ‘%s’ expects type ‘char *’, but argument 3 has type ‘void *’
actions.c: In function ‘transformClusterAttribute’:
actions.c:3970: warning: format ‘%s’ expects type ‘char *’, but argument 3 has type ‘void *’
actions.c:3974: warning: format ‘%s’ expects type ‘char *’, but argument 3 has type ‘void *’
actions.c:4236: warning: format ‘%s’ expects type ‘char *’, but argument 3 has type ‘void *’
actions.c:4248: warning: format ‘%s’ expects type ‘char *’, but argument 3 has type ‘void *’
actions.c:4260: warning: format ‘%s’ expects type ‘char *’, but argument 3 has type ‘void *’
actions.c:4266: warning: format ‘%s’ expects type ‘char *’, but argument 3 has type ‘void *’
actions.c:4269: warning: format ‘%s’ expects type ‘char *’, but argument 3 has type ‘void *’
actions.c: In function ‘transformDihedralCluster’:
actions.c:6356: warning: format ‘%i’ expects type ‘int’, but argument 6 has type ‘long int’
actions.c:6440: warning: format ‘%6i’ expects type ‘int’, but argument 3 has type ‘long int’
actions.c:6481: warning: format ‘%6i’ expects type ‘int’, but argument 3 has type ‘long int’
actions.c:6541: warning: format ‘%10li’ expects type ‘long int’, but argument 4 has type ‘int’
actions.c:6564: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘long int’
mpicc -c -m64 -DBINTRAJ -DMPI   -o analyze.o analyze.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o thermo.o thermo.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o pubfft.o pubfft.c
mpicc -c -m64 -DBINTRAJ -DMPI   -o cluster.o cluster.c
cluster.c: In function ‘SymmetricMatrixDistribution’:
cluster.c:275: warning: unknown conversion type character ‘(’ in format
cluster.c:276: warning: unknown conversion type character ‘(’ in format
cluster.c:279: warning: unknown conversion type character ‘(’ in format
cluster.c:280: warning: unknown conversion type character ‘(’ in format
cluster.c: In function ‘OutputIntermediateClusters’:
cluster.c:1178: warning: format ‘%s’ expects type ‘char *’, but argument 3 has type ‘void *’
cluster.c: In function ‘ClusteringMergeNames’:
cluster.c:1243: warning: format not a string literal and no format arguments
cluster.c: In function ‘PtrajClusteringSecondPassOutputInfo’:
cluster.c:4099: warning: format ‘%s’ expects type ‘char *’, but argument 3 has type ‘void *’
cluster.c:4101: warning: format ‘%s’ expects type ‘char *’, but argument 3 has type ‘void *’
cluster.c: In function ‘PtrajClusteringOutputHeaderToFile’:
cluster.c:4321: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘time_t’
cluster.c:4322: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘time_t’
cluster.c:4324: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘time_t’
cluster.c:4326: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘time_t’
cluster.c: In function ‘PtrajClusteringOutputClusterInfo’:
cluster.c:4570: warning: format ‘%s’ expects type ‘char *’, but argument 3 has type ‘void *’
cluster.c:4584: warning: format ‘%s’ expects type ‘char *’, but argument 3 has type ‘void *’
cluster.c:4662: warning: format ‘%s’ expects type ‘char *’, but argument 3 has type ‘void *’
cluster.c:4712: warning: format ‘%s’ expects type ‘char *’, but argument 3 has type ‘void *’
cluster.c:4727: warning: format ‘%s’ expects type ‘char *’, but argument 3 has type ‘void *’
cluster.c: In function ‘printClusterNodes’:
cluster.c:7981: warning: format ‘%x’ expects type ‘unsigned int’, but argument 3 has type ‘struct ClusterNode *’
cluster.c:7983: warning: format ‘%x’ expects type ‘unsigned int’, but argument 3 has type ‘struct PtrajCluster *’
cluster.c:7987: warning: format ‘%x’ expects type ‘unsigned int’, but argument 3 has type ‘struct ClusterNode *’
cluster.c: In function ‘printClusters’:
cluster.c:8000: warning: format ‘%x’ expects type ‘unsigned int’, but argument 3 has type ‘struct ClusterNode *’
cluster.c:8001: warning: format ‘%x’ expects type ‘unsigned int’, but argument 2 has type ‘struct PtrajCluster *’
cluster.c:8006: warning: format ‘%x’ expects type ‘unsigned int’, but argument 2 has type ‘struct ClusterNode *’
mpicc -c -m64 -DBINTRAJ -DMPI   -o clusterLib.o clusterLib.c
mpicc  -o rdparm main.o rdparm.o dispatch.o help.o utility.o second.o io.o trajectory.o evec.o torsion.o mask.o rms.o display.o interface.o energy.o experimental.o ptraj.o actions.o analyze.o thermo.o pubfft.o cluster.o clusterLib.o /home/userid/Documents/amber10/lib/libpdb.a /home/userid/Documents/amber10/lib/libsym.a /home/userid/Documents/amber10/lib/arpack.a /home/userid/Documents/amber10/lib/lapack.a /home/userid/Documents/amber10/lib/blas.a /home/userid/Documents/amber10/lib/f2c.a    -lmpi ../netcdf/lib/libnetcdf.a -lm
mpicc  -o ptraj main.o rdparm.o dispatch.o help.o utility.o second.o io.o trajectory.o evec.o torsion.o mask.o rms.o display.o interface.o energy.o experimental.o ptraj.o actions.o analyze.o thermo.o pubfft.o cluster.o clusterLib.o /home/userid/Documents/amber10/lib/libpdb.a /home/userid/Documents/amber10/lib/libsym.a /home/userid/Documents/amber10/lib/arpack.a /home/userid/Documents/amber10/lib/lapack.a /home/userid/Documents/amber10/lib/blas.a /home/userid/Documents/amber10/lib/f2c.a    -lmpi ../netcdf/lib/libnetcdf.a -lm
/bin/mv rdparm ptraj /home/userid/Documents/amber10/bin
make[1]: Leaving directory `/home/userid/Documents/amber10/src/ptraj'
(cd reduce && make install )
make[1]: Entering directory `/home/userid/Documents/amber10/src/reduce'
installing /toolclasses...
make[2]: Entering directory `/home/userid/Documents/amber10/src/reduce/toolclasses'
g++ -O  -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c UseCount.cpp -o UseCount.o
g++ -O  -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c Point3d.cpp -o Point3d.o
g++ -O  -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c Stringclass.cpp -o Stringclass.o
g++ -O  -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c Hash.cpp -o Hash.o
g++ -O  -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c utility.cpp -o utility.o
g++ -O  -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c column_sprintf.cpp -o column_sprintf.o
g++ -O  -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c column_sscanf.cpp -o column_sscanf.o
g++ -O  -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c DisjointSets.cpp -o DisjointSets.o
Loading libtoolclasses.a ... 
done

make[2]: Leaving directory `/home/userid/Documents/amber10/src/reduce/toolclasses'
installing /libpdb...
make[2]: Entering directory `/home/userid/Documents/amber10/src/reduce/libpdb'
g++ -O  -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb_read.cpp -o pdb_read.o
g++ -O  -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb_sprntf.cpp -o pdb_sprntf.o
g++ -O  -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb_sscanf.cpp -o pdb_sscanf.o
g++ -O  -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb_chars.cpp -o pdb_chars.o
g++ -O  -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb_type.cpp -o pdb_type.o
g++ -O  -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb++.cpp -o pdb++.o
g++ -O  -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdbinput.cpp -o pdbinput.o
Loading libpdb++.a ... 
done

make[2]: Leaving directory `/home/userid/Documents/amber10/src/reduce/libpdb'
installing /reduce_src...
make[2]: Entering directory `/home/userid/Documents/amber10/src/reduce/reduce_src'
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o GraphToHoldScores.o GraphToHoldScores.cpp
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o reduce.o reduce.cpp
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o CTab.o CTab.cpp
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o ElementInfo.o ElementInfo.cpp
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o StdResH.o StdResH.cpp
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o ResBlk.o ResBlk.cpp
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o AtomConn.o AtomConn.cpp
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o AtomPositions.o AtomPositions.cpp
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o DotSph.o DotSph.cpp
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o Mover.o Mover.cpp
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o RotMethyl.o RotMethyl.cpp
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o RotDonor.o RotDonor.cpp
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o FlipMemo.o FlipMemo.cpp
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o CliqueList.o CliqueList.cpp
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o AtomDescr.o AtomDescr.cpp
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o PDBrec.o PDBrec.cpp
g++ -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o MoveableNode.o MoveableNode.cpp
mpicc -c -O3  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"/home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt"' -I../libpdb -I../toolclasses  -o hybrid_36_c.o hybrid_36_c.c
g++ -o reduce GraphToHoldScores.o reduce.o CTab.o ElementInfo.o StdResH.o ResBlk.o AtomConn.o AtomPositions.o DotSph.o Mover.o RotMethyl.o RotDonor.o FlipMemo.o CliqueList.o AtomDescr.o PDBrec.o MoveableNode.o hybrid_36_c.o -L../libpdb -lpdb++ -L../toolclasses -ltoolclasses -lm
mv reduce /home/userid/Documents/amber10/bin
gunzip -c -d ../reduce_wwPDB_het_dict.txt.gz > /home/userid/Documents/amber10/dat/reduce_wwPDB_het_dict.txt
make[2]: Leaving directory `/home/userid/Documents/amber10/src/reduce/reduce_src'
make[1]: Leaving directory `/home/userid/Documents/amber10/src/reduce'
(cd leap && make install )
make[1]: Entering directory `/home/userid/Documents/amber10/src/leap'
Compiling basic programs
cd src/leap; make installteLeap
make[2]: Entering directory `/home/userid/Documents/amber10/src/leap/src/leap'
mpicc -c -m64 -DBINTRAJ -DMPI  -o basics.o basics.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o sysdepend.o sysdepend.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o stringExtra.o stringExtra.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o varArray.o varArray.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o getline.o getline.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o avl.o avl.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o pdb_format.o pdb_format.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o pdb_read.o pdb_read.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o pdb_sprntf.o pdb_sprntf.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o pdb_sscanf.o pdb_sscanf.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o pdb_write.o pdb_write.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o vector.o vector.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o zMatrix.o zMatrix.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o sort.o sort.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o bag.o bag.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o hash.o hash.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o dictionary.o dictionary.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o database.o database.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o nVector.o nVector.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o ring.o ring.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o matrix.o matrix.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o fortran.o fortran.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o displayer.o displayer.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o assoc.o assoc.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o atom.o atom.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o byteArray.o byteArray.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o collection.o collection.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o container.o container.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o internal.o internal.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o list.o list.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o loop.o loop.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o molecule.o molecule.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o oDouble.o oDouble.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o oInteger.o oInteger.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o oString.o oString.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o objekt.o objekt.c
objekt.c: In function ‘Destroy’:
objekt.c:251: warning: format ‘%x’ expects type ‘unsigned int’, but argument 4 has type ‘OBJEKT’
mpicc -c -m64 -DBINTRAJ -DMPI  -o parmSet.o parmSet.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o residue.o residue.c
residue.c: In function ‘ResidueConnect’:
residue.c:336: warning: passing argument 1 of ‘AtomBondTo’ from incompatible pointer type
residue.c:336: warning: passing argument 2 of ‘AtomBondTo’ from incompatible pointer type
residue.c: In function ‘ResidueMutate’:
residue.c:464: warning: passing argument 1 of ‘BuildFixInternals’ from incompatible pointer type
mpicc -c -m64 -DBINTRAJ -DMPI  -o unit.o unit.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o unitio.o unitio.c
unitio.c: In function ‘zUnitIOSaveAmberParmFormat’:
unitio.c:4056: warning: passing argument 1 of ‘SortByInteger’ from incompatible pointer type
unitio.c:4056: warning: passing argument 4 of ‘SortByInteger’ from incompatible pointer type
unitio.c: In function ‘zUnitIOSaveAmberParmFormat_old’:
unitio.c:6069: warning: passing argument 1 of ‘SortByInteger’ from incompatible pointer type
unitio.c:6069: warning: passing argument 4 of ‘SortByInteger’ from incompatible pointer type
mpicc -c -m64 -DBINTRAJ -DMPI  -o tripos.o tripos.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o graphUtil.o graphUtil.c
graphUtil.c: In function ‘GraphUtilFindAllSmallestRingsAndRingGroups’:
graphUtil.c:675: warning: passing argument 1 of ‘SortByInteger’ from incompatible pointer type
graphUtil.c:675: warning: passing argument 4 of ‘SortByInteger’ from incompatible pointer type
mpicc -c -m64 -DBINTRAJ -DMPI  -o select.o select.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o amber.o amber.c
amber.c: In function ‘uAmberReadUnitFromPrep’:
amber.c:986: warning: passing argument 1 of ‘SortByInteger’ from incompatible pointer type
amber.c:986: warning: passing argument 4 of ‘SortByInteger’ from incompatible pointer type
mpicc -c -m64 -DBINTRAJ -DMPI  -o build.o build.c
build.c: In function ‘bBuildFlipChiralityFor’:
build.c:1901: warning: passing argument 1 of ‘SortByInteger’ from incompatible pointer type
build.c:1901: warning: passing argument 4 of ‘SortByInteger’ from incompatible pointer type
build.c:1907: warning: passing argument 1 of ‘GraphUtilFindAllSmallestRings’ from incompatible pointer type
build.c: In function ‘BuildInternalsForSimpleRings’:
build.c:2185: warning: passing argument 1 of ‘GraphUtilFindAllSmallestRingsAndRingGroups’ from incompatible pointer type
mpicc -c -m64 -DBINTRAJ -DMPI  -o elements.o elements.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o library.o library.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o chirality.o chirality.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o minimizer.o minimizer.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o model.o model.c
model.c: In function ‘zModelOrderAtoms’:
model.c:497: warning: passing argument 1 of ‘Sift’ from incompatible pointer type
mpicc -c -m64 -DBINTRAJ -DMPI  -o parmLib.o parmLib.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o pdbFile.o pdbFile.c
pdbFile.c: In function ‘zPdbBuildCoordinatesForContainer’:
pdbFile.c:1091: warning: passing argument 1 of ‘BuildFixInternals’ from incompatible pointer type
pdbFile.c: In function ‘zPdbAddAtom’:
pdbFile.c:1210: warning: passing argument 1 of ‘BuildInternalsForContainer’ from incompatible pointer type
pdbFile.c: In function ‘writeTER’:
pdbFile.c:1764: warning: initialization from incompatible pointer type
mpicc -c -m64 -DBINTRAJ -DMPI  -o mol2File.o mol2File.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o tools.o tools.c
tools.c: In function ‘iToolDistanceSearch’:
tools.c:1643: warning: passing argument 1 of ‘SortByDouble’ from incompatible pointer type
tools.c:1643: warning: passing argument 4 of ‘SortByDouble’ from incompatible pointer type
tools.c: In function ‘ToolOrientPrincipleAxisAlongCoordinateAxis’:
tools.c:1714: warning: passing argument 2 of ‘MathOpDiagonalize’ from incompatible pointer type
mpicc -c -m64 -DBINTRAJ -DMPI  -o variables.o variables.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o parser.o parser.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o help.o help.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o utilMakeHelp.o utilMakeHelp.c
mpicc -o utilMakeHelp basics.o sysdepend.o stringExtra.o varArray.o getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o  pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o  dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o utilMakeHelp.o -lm
./utilMakeHelp helptext.text helptext.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o helptext.o helptext.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o octree.o octree.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o commands.o commands.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o mathop.o mathop.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o block.o block.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o restraint.o restraint.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o hybrid.o hybrid.c
mpicc -c -m64 -DBINTRAJ -DMPI  -o tLeap.o tLeap.c
mpicc  -o teLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o  pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o  dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o  collection.o container.o internal.o list.o loop.o molecule.o  oDouble.o oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o tripos.o graphUtil.o select.o amber.o build.o elements.o library.o chirality.o minimizer.o model.o parmLib.o pdbFile.o mol2File.o tools.o variables.o parser.o help.o helptext.o octree.o commands.o mathop.o block.o restraint.o hybrid.o tLeap.o -lm
mv teLeap ../../../../exe
make[2]: Leaving directory `/home/userid/Documents/amber10/src/leap/src/leap'
Copying shell script
sed -e "s?BINDIR?/home/userid/Documents/amber10/bin?" -e "s?DATDIR?/home/userid/Documents/amber10/dat?;" tleap > /home/userid/Documents/amber10/bin/tleap
chmod +x /home/userid/Documents/amber10/bin/tleap
make skip_xleap
make[2]: Entering directory `/home/userid/Documents/amber10/src/leap'
NOTE: skipping the building of xleap as X11 libraries are not installed or
NOTE: -nox11 was specified as an option to configure.
make[2]: Leaving directory `/home/userid/Documents/amber10/src/leap'
make[1]: Leaving directory `/home/userid/Documents/amber10/src/leap'
(cd gleap && make install )
make[1]: Entering directory `/home/userid/Documents/amber10/src/gleap'
cd freelib; make
make[2]: Entering directory `/home/userid/Documents/amber10/src/gleap/freelib'
cd readline; make
make[3]: Entering directory `/home/userid/Documents/amber10/src/gleap/freelib/readline'
Makefile:134: warning: overriding commands for target `.c.o'
../../../config.h:99: warning: ignoring old commands for target `.c.o'
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o bind.o bind.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o callback.o callback.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o compat.o compat.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o complete.o complete.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o display.o display.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o funmap.o funmap.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o histexpand.o histexpand.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o histfile.o histfile.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o history.o history.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o histsearch.o histsearch.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o input.o input.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o isearch.o isearch.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o keymaps.o keymaps.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o kill.o kill.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o macro.o macro.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o mbutil.o mbutil.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o misc.o misc.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o nls.o nls.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o parens.o parens.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o readline.o readline.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o rltty.o rltty.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o savestring.o savestring.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o search.o search.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o shell.o shell.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o signals.o signals.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o termcap.o termcap.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o terminal.o terminal.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o text.o text.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o tilde.o tilde.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o tparam.o tparam.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o undo.o undo.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o util.o util.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o version.o version.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o vi_mode.o vi_mode.c
mpicc -c -m64 -DBINTRAJ -DMPI  -DHAVE_CONFIG_H -I. -o xmalloc.o xmalloc.c
rm -f libreadline.a
ar cqs libreadline.a bind.o callback.o compat.o complete.o display.o funmap.o histexpand.o histfile.o history.o histsearch.o input.o isearch.o keymaps.o kill.o macro.o mbutil.o misc.o nls.o parens.o readline.o rltty.o savestring.o search.o shell.o signals.o termcap.o terminal.o text.o tilde.o tparam.o undo.o util.o version.o vi_mode.o xmalloc.o
make[3]: Leaving directory `/home/userid/Documents/amber10/src/gleap/freelib/readline'
make[2]: Leaving directory `/home/userid/Documents/amber10/src/gleap/freelib'
cd mortsrc; make
make[2]: Entering directory `/home/userid/Documents/amber10/src/gleap/mortsrc'
cd common;make
make[3]: Entering directory `/home/userid/Documents/amber10/src/gleap/mortsrc/common'
g++ -c -O2 -Wall -W -D_REENTRANT  -I../../freelib -I../../freelib -o  numvec.o   numvec.cpp
numvec.cpp: In function ‘double mort::normal(const mort::numvec&)’:
numvec.cpp:124: warning: comparison between signed and unsigned integer expressions
numvec.cpp: In function ‘double mort::dot(const mort::numvec&, const mort::numvec&)’:
numvec.cpp:159: warning: comparison between signed and unsigned integer expressions
numvec.cpp: In function ‘void mort::jacobi(mort::matrix&, mort::numvec&, mort::matrix&, int&)’:
numvec.cpp:424: warning: comparison between signed and unsigned integer expressions
g++ -c -O2 -Wall -W -D_REENTRANT  -I../../freelib -I../../freelib -o  pertab.o   pertab.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I../../freelib -I../../freelib -o  fortran.o   fortran.cpp
fortran.cpp: In member function ‘void mort::format::write(std::ostream&) const’:
fortran.cpp:133: warning: comparison between signed and unsigned integer expressions
fortran.cpp:138: warning: comparison between signed and unsigned integer expressions
fortran.cpp:145: warning: comparison between signed and unsigned integer expressions
fortran.cpp:153: warning: comparison between signed and unsigned integer expressions
g++ -c -O2 -Wall -W -D_REENTRANT  -I../../freelib -I../../freelib -o  hashcode.o   hashcode.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I../../freelib -I../../freelib -o  algorithm.o   algorithm.cpp
rm -f libcommon.a
ar cqs libcommon.a numvec.o pertab.o fortran.o hashcode.o algorithm.o
make[3]: Leaving directory `/home/userid/Documents/amber10/src/gleap/mortsrc/common'
cd object;make
make[3]: Entering directory `/home/userid/Documents/amber10/src/gleap/mortsrc/object'
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  adjacency.o   adjacency.cpp
adjacency.cpp: In member function ‘bool mort::adjacency_t::empty() const’:
adjacency.cpp:86: warning: comparison between signed and unsigned integer expressions
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  addhs.o   addhs.cpp
addhs.cpp: In function ‘bool mort::too_close(const std::vector<std::valarray<double>, std::allocator<std::valarray<double> > >&, const mort::numvec&, double)’:
addhs.cpp:74: warning: comparison between signed and unsigned integer expressions
addhs.cpp: In function ‘void mort::addHs(mort::moref_t&)’:
addhs.cpp:203: warning: comparison between signed and unsigned integer expressions
addhs.cpp: In function ‘void mort::addHs(mort::molecule_t&)’:
addhs.cpp:218: warning: comparison between signed and unsigned integer expressions
addhs.cpp:220: warning: comparison between signed and unsigned integer expressions
addhs.cpp: In function ‘void mort::addHs(mort::atomvec_t&)’:
addhs.cpp:232: warning: comparison between signed and unsigned integer expressions
addhs.cpp:237: warning: comparison between signed and unsigned integer expressions
addhs.cpp:239: warning: comparison between signed and unsigned integer expressions
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  atomexpr.o   atomexpr.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  atomfun.o   atomfun.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  bondfun.o   bondfun.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  atomvec.o   atomvec.cpp
atomvec.cpp: In member function ‘bool mort::atomvec_t::is_arom() const’:
atomvec.cpp:152: warning: suggest a space before ‘;’ or explicit braces around empty body in ‘for’ statement
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  component.o   component.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  database.o   database.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  entity.o   entity.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  finder.o   finder.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  fixbo.o   fixbo.cpp
fixbo.cpp:464: warning: unused parameter ‘atms’
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  molecule.o   molecule.cpp
molecule.cpp: In member function ‘void mort::molecule_t::remove_atom(const mort::moref_t&)’:
molecule.cpp:407: warning: comparison between signed and unsigned integer expressions
molecule.cpp:413: warning: comparison between signed and unsigned integer expressions
molecule.cpp:419: warning: comparison between signed and unsigned integer expressions
molecule.cpp:425: warning: comparison between signed and unsigned integer expressions
molecule.cpp:431: warning: comparison between signed and unsigned integer expressions
molecule.cpp: In member function ‘void mort::molecule_t::remove_resd(const mort::moref_t&)’:
molecule.cpp:460: warning: comparison between signed and unsigned integer expressions
molecule.cpp: In function ‘void mort::print_vec(std::ostream&, const std::vector<int, std::allocator<int> >&)’:
molecule.cpp:477: warning: comparison between signed and unsigned integer expressions
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  molfun.o   molfun.cpp
molfun.cpp: In function ‘void mort::assign_ring(mort::moref_t&)’:
molfun.cpp:83: warning: comparison between signed and unsigned integer expressions
molfun.cpp: In function ‘void mort::assign_arom(mort::moref_t&)’:
molfun.cpp:139: warning: comparison between signed and unsigned integer expressions
molfun.cpp: In function ‘void mort::setpchg(mort::molecule_t&)’:
molfun.cpp:506: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result
molfun.cpp:513: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  moref.o   moref.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  moiter.o   moiter.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  namemap.o   namemap.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  parmfun.o   parmfun.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  resdfun.o   resdfun.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  ring.o   ring.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I.. -I../../freelib -o  subst.o   subst.cpp
subst.cpp: In member function ‘virtual void mort::subst_finder::list_next(const mort::atomvec_t&, mort::atomvec_t&)’:
subst.cpp:81: warning: comparison between signed and unsigned integer expressions
make[3]: Leaving directory `/home/userid/Documents/amber10/src/gleap/mortsrc/object'
cd ambfmt;make
make[3]: Entering directory `/home/userid/Documents/amber10/src/gleap/mortsrc/ambfmt'
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  ambfrc-amber.o   ambfrc-amber.cpp
ambfrc-amber.cpp: In function ‘void mort::ambfrc::amber::skip_hydro(std::istream&)’:
ambfrc-amber.cpp:23: warning: suggest a space before ‘;’ or explicit braces around empty body in ‘while’ statement
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  ambfrc-amoeba.o   ambfrc-amoeba.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  amboff.o   amboff.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  chain.o   chain.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  exclude.o   exclude.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  extent.o   extent.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  les.o   les.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  parm.o   parm.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  parmset.o   parmset.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  prep.o   prep.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  prmtop-amoeba.o   prmtop-amoeba.cpp
prmtop-amoeba.cpp: In function ‘void mort::prmtop::amoeba::setup_adjust(const mort::molecule_t&, mort::excl_t&, const mort::molecule_t&)’:
prmtop-amoeba.cpp:1079: warning: suggest a space before ‘;’ or explicit braces around empty body in ‘for’ statement
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  prmtop.o   prmtop.cpp
prmtop.cpp: In function ‘void mort::prmtop::write_excl_size(const mort::excl_t&, std::ostream&)’:
prmtop.cpp:242: warning: comparison between signed and unsigned integer expressions
prmtop.cpp: In function ‘void mort::prmtop::write_vdw_index(std::ostream&, int)’:
prmtop.cpp:278: warning: comparison between signed and unsigned integer expressions
prmtop.cpp: In function ‘void mort::prmtop::write_excl_list(const mort::excl_t&, std::ostream&)’:
prmtop.cpp:677: warning: comparison between signed and unsigned integer expressions
make[3]: Leaving directory `/home/userid/Documents/amber10/src/gleap/mortsrc/ambfmt'
cd atmask;make
make[3]: Entering directory `/home/userid/Documents/amber10/src/gleap/mortsrc/atmask'
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  atom.o   atom.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  condition.o   condition.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  dist.o   dist.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  logic.o   logic.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  mask.o   mask.cpp
mask.cpp:37: warning: unused parameter ‘reg’
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  paren.o   paren.cpp
paren.cpp:14: warning: unused parameter ‘mol’
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  resd.o   resd.cpp
make[3]: Leaving directory `/home/userid/Documents/amber10/src/gleap/mortsrc/atmask'
cd capbox;make
make[3]: Entering directory `/home/userid/Documents/amber10/src/gleap/mortsrc/capbox'
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  addions.o   addions.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  octree.o   octree.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  shaper.o   shaper.cpp
shaper.cpp: In member function ‘void mort::capbox::solvent_shaper::make_exclusion_list(double)’:
shaper.cpp:67: warning: comparison between signed and unsigned integer expressions
shaper.cpp: In member function ‘virtual int mort::capbox::solvent_shaper::check_box(const mort::numvec&, const mort::numvec&, double)’:
shaper.cpp:173: warning: comparison between signed and unsigned integer expressions
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  solvate.o   solvate.cpp
make[3]: Leaving directory `/home/userid/Documents/amber10/src/gleap/mortsrc/capbox'
cd enefrc;make
make[3]: Entering directory `/home/userid/Documents/amber10/src/gleap/mortsrc/enefrc'
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  bonding.o   bonding.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  ctrlparm.o   ctrlparm.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  nonbond-lst.o   nonbond-lst.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  nonbond-egb.o   nonbond-egb.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I.. -I../../freelib -I. -I.. -I../../freelib -I. -o  nonbond-pbc.o   nonbond-pbc.cpp
make[3]: Leaving directory `/home/userid/Documents/amber10/src/gleap/mortsrc/enefrc'
cd guilib;make
make[3]: Entering directory `/home/userid/Documents/amber10/src/gleap/mortsrc/guilib'
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  command.o   command.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  console.o   console.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  control.o   control.cpp
control.cpp: In function ‘void mort::interpret(std::string, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)’:
control.cpp:44: warning: comparison between signed and unsigned integer expressions
control.cpp:53: warning: comparison between signed and unsigned integer expressions
control.cpp:53: warning: comparison between signed and unsigned integer expressions
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  grammar.o   grammar.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  leaplog.o   leaplog.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  mainwin.o   mainwin.cpp
make[3]: Leaving directory `/home/userid/Documents/amber10/src/gleap/mortsrc/guilib'
cd format;make
make[3]: Entering directory `/home/userid/Documents/amber10/src/gleap/mortsrc/format'
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  ambfrc.o   ambfrc.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  amboff.o   amboff.cpp
amboff.cpp: In function ‘bool mort::read_off(std::istream&, mort::molecule_t&)’:
amboff.cpp:13: warning: suggest a space before ‘;’ or explicit braces around empty body in ‘while’ statement
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  format.o   format.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  mdlfmt.o   mdlfmt.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  pdbent.o   pdbent.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  prmtop.o   prmtop.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  smarts.o   smarts.cpp
In file included from /usr/include/c++/4.3/ext/hash_map:64,
                 from ../smarts.hpp:6,
                 from smarts.cpp:3:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  tripos.o   tripos.cpp
make[3]: Leaving directory `/home/userid/Documents/amber10/src/gleap/mortsrc/format'
cd smarts;make
make[3]: Entering directory `/home/userid/Documents/amber10/src/gleap/mortsrc/smarts'
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  parse.o   parse.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  reader.o   reader.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  status.o   status.cpp
make[3]: Leaving directory `/home/userid/Documents/amber10/src/gleap/mortsrc/smarts'
cd tripos;make
make[3]: Entering directory `/home/userid/Documents/amber10/src/gleap/mortsrc/tripos'
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  atom.o   atom.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  bond.o   bond.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  head.o   head.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  resd.o   resd.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  sect.o   sect.cpp
make[3]: Leaving directory `/home/userid/Documents/amber10/src/gleap/mortsrc/tripos'
cd pdbent;make
make[3]: Entering directory `/home/userid/Documents/amber10/src/gleap/mortsrc/pdbent'
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  atom.o   atom.cpp
atom.cpp: In function ‘void mort::pdbent::read_bond(std::istream&, mort::molecule_t&)’:
atom.cpp:99: warning: comparison between signed and unsigned integer expressions
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  build.o   build.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I.. -I../../freelib -I. -I.. -I../../freelib -o  second.o   second.cpp
make[3]: Leaving directory `/home/userid/Documents/amber10/src/gleap/mortsrc/pdbent'
cd nablib;make
make[3]: Entering directory `/home/userid/Documents/amber10/src/gleap/mortsrc/nablib'
Makefile:4: warning: overriding commands for target `.c.o'
../../../config.h:99: warning: ignoring old commands for target `.c.o'
g++ -c boundsutil.cpp -I../../mortsrc -I../../freelib
boundsutil.cpp: In function ‘BOUNDS_T* bsetup(mort::molecule_t&)’:
boundsutil.cpp:153: warning: deprecated conversion from string constant to ‘char*’
boundsutil.cpp:153: warning: deprecated conversion from string constant to ‘char*’
boundsutil.cpp:168: warning: deprecated conversion from string constant to ‘char*’
boundsutil.cpp:168: warning: deprecated conversion from string constant to ‘char*’
boundsutil.cpp:195: warning: deprecated conversion from string constant to ‘char*’
boundsutil.cpp:195: warning: deprecated conversion from string constant to ‘char*’
boundsutil.cpp:202: warning: deprecated conversion from string constant to ‘char*’
boundsutil.cpp:202: warning: deprecated conversion from string constant to ‘char*’
boundsutil.cpp:208: warning: deprecated conversion from string constant to ‘char*’
boundsutil.cpp:208: warning: deprecated conversion from string constant to ‘char*’
boundsutil.cpp: In function ‘void read_bdb(int*, BDBENT*)’:
boundsutil.cpp:547: warning: format ‘%f’ expects type ‘float*’, but argument 4 has type ‘double*’
boundsutil.cpp:547: warning: format ‘%f’ expects type ‘float*’, but argument 5 has type ‘double*’
boundsutil.cpp:547: warning: format ‘%f’ expects type ‘float*’, but argument 6 has type ‘double*’
boundsutil.cpp:547: warning: format ‘%f’ expects type ‘float*’, but argument 7 has type ‘double*’
boundsutil.cpp:547: warning: format ‘%f’ expects type ‘float*’, but argument 8 has type ‘double*’
boundsutil.cpp: In function ‘int rd_bmat(char*, BOUNDS_T*, int)’:
boundsutil.cpp:648: warning: format ‘%f’ expects type ‘float*’, but argument 5 has type ‘double*’
boundsutil.cpp:648: warning: format ‘%f’ expects type ‘float*’, but argument 6 has type ‘double*’
mpicc -c -Dflex -DMORT -O3 -m64 -DBINTRAJ  -DMPI  -o binpos.o binpos.c
binpos.c: In function ‘writebinposhdr’:
binpos.c:61: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
binpos.c: In function ‘writebinposfrm’:
binpos.c:70: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
binpos.c:79: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
mpicc -c -Dflex -DMORT -O3 -m64 -DBINTRAJ  -DMPI  -o conjgrad.o conjgrad.c
mpicc -c -Dflex -DMORT -O3 -m64 -DBINTRAJ  -DMPI  -o memutil.o memutil.c
memutil.c: In function ‘vector’:
memutil.c:31: warning: format ‘%lld’ expects type ‘long long int’, but argument 3 has type ‘size_t’
g++ -c molsurf.cpp -I../../mortsrc -I../../freelib
mpicc -c -Dflex -DMORT -O3 -m64 -DBINTRAJ  -DMPI  -o prm.o prm.c
prm.c: In function ‘readparm’:
prm.c:449: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:495: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:587: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:608: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:628: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:645: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:662: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:694: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:713: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:734: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:755: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:776: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:797: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:818: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:844: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:865: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:887: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:909: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:932: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:955: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:979: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:1005: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:1032: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:1060: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:1083: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:1101: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:1122: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:1144: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:1183: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:1202: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:1286: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:1295: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:1321: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
prm.c:1336: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
mpicc -c -Dflex -DMORT -O3 -m64 -DBINTRAJ  -DMPI  -o rand2.o rand2.c
flex -t mm_options.l | sed -e 's/yy/mmo/g' -e 's/stdout/nabout/' > lex.mm_options.c
mpicc -c -Dflex -DMORT -O3 -m64 -DBINTRAJ  -DMPI  -o sff.o sff.c
In file included from eff.c:1666,
                 from sff.c:795:
gbsa.c: In function ‘egb’:
gbsa.c:177: warning: too few arguments for format
In file included from sff.c:800:
mask.c: In function ‘set_belly_mask’:
mask.c:72: warning: cast to pointer from integer of different size
mpicc -c -Dflex -DMORT -O3 -m64 -DBINTRAJ  -DMPI  -o time.o time.c
mpicc -c -Dflex -DMORT -O3 -m64 -DBINTRAJ  -DMPI  -o traceback.o traceback.c
traceback.c: In function ‘rt_errormsg’:
traceback.c:14: warning: format not a string literal and no format arguments
make[3]: Leaving directory `/home/userid/Documents/amber10/src/gleap/mortsrc/nablib'
rm -f libmort.a
ar cqs libmort.a ambfmt/ambfrc-amber.o   ambfmt/ambfrc-amoeba.o  ambfmt/amboff.o ambfmt/chain.o          ambfmt/exclude.o        ambfmt/extent.o ambfmt/les.o            ambfmt/parm.o           ambfmt/parmset.o ambfmt/prmtop-amoeba.o  ambfmt/prmtop.o         ambfmt/prep.o atmask/atom.o           atmask/condition.o      atmask/dist.o atmask/logic.o          atmask/mask.o           atmask/paren.o atmask/resd.o capbox/addions.o        capbox/octree.o         capbox/solvate.o capbox/shaper.o common/numvec.o         common/pertab.o         common/fortran.o common/hashcode.o       common/algorithm.o enefrc/bonding.o        enefrc/ctrlparm.o       enefrc/nonbond-egb.o enefrc/nonbond-lst.o    enefrc/nonbond-pbc.o format/ambfrc.o         format/amboff.o         format/format.o format/mdlfmt.o         format/pdbent.o         format/prmtop.o format/smarts.o         format/tripos.o guilib/command.o        guilib/console.o guilib/control.o        guilib/mainwin.o        guilib/grammar.o guilib/leaplog.o object/adjacency.o      object/entity.o         object/finder.o object/atomexpr.o       object/atomfun.o        object/bondfun.o object/atomvec.o        object/component.o      object/database.o object/moiter.o         object/molecule.o       object/molfun.o object/parmfun.o        object/moref.o          object/resdfun.o object/ring.o           object/subst.o          object/namemap.o object/fixbo.o	    object/addhs.o pdbent/atom.o           pdbent/build.o          pdbent/second.o smarts/parse.o          smarts/reader.o         smarts/status.o tripos/atom.o           tripos/bond.o           tripos/head.o tripos/resd.o           tripos/sect.o nablib/binpos.o         nablib/conjgrad.o       nablib/memutil.o nablib/prm.o            nablib/rand2.o          nablib/sff.o nablib/time.o           nablib/traceback.o      nablib/boundsutil.o nablib/molsurf.o
make[2]: Leaving directory `/home/userid/Documents/amber10/src/gleap/mortsrc'
cd plugins; make
make[2]: Entering directory `/home/userid/Documents/amber10/src/gleap/plugins'
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  add.o   add.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  addmap.o   addmap.cpp
addmap.cpp: In member function ‘virtual bool amber::addmap_command::exec()’:
addmap.cpp:35: warning: comparison between signed and unsigned integer expressions
addmap.cpp:41: warning: comparison between signed and unsigned integer expressions
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  addions.o   addions.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  bond.o   bond.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  center.o   center.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  charge.o   charge.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  copy.o   copy.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  create.o   create.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  desc.o   desc.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  delete.o   delete.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  energy.o   energy.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  geom.o   geom.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  help.o   help.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  impose.o   impose.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  list.o   list.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  loadcrd.o   loadcrd.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  loadfrc.o   loadfrc.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  loadmol2.o   loadmol2.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  loadoff.o   loadoff.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  loadpdb.o   loadpdb.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  loadprep.o   loadprep.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  loadsdf.o   loadsdf.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  measure.o   measure.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  merge.o   merge.cpp
g++ -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib   -c -o moloper.o moloper.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  savemol2.o   savemol2.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  saveoff.o   saveoff.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  savepdb.o   savepdb.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  saveprm.o   saveprm.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  savesdf.o   savesdf.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  set.o   set.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  shell.o   shell.cpp
shell.cpp: In member function ‘virtual bool amber::shell_command::exec()’:
shell.cpp:23: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result
shell.cpp:27: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  solvate.o   solvate.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  source.o   source.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -I. -I../mortsrc -I../mortsrc/guilib -I../freelib -o  zmatrix.o   zmatrix.cpp
rm -f libplugins.a
ar cqs libplugins.a add.o addmap.o addions.o bond.o center.o charge.o copy.o create.o desc.o delete.o energy.o geom.o help.o impose.o list.o loadcrd.o loadfrc.o loadmol2.o loadoff.o loadpdb.o loadprep.o loadsdf.o measure.o merge.o moloper.o savemol2.o saveoff.o savepdb.o saveprm.o savesdf.o set.o shell.o solvate.o source.o zmatrix.o
make[2]: Leaving directory `/home/userid/Documents/amber10/src/gleap/plugins'
cd leapsrc; BINDIR=/home/userid/Documents/amber10/bin  make install
make[2]: Entering directory `/home/userid/Documents/amber10/src/gleap/leapsrc'
g++ -c -O2 -Wall -W -D_REENTRANT  -I../mortsrc -I../mortsrc/guilib -I../plugins -I../freelib -I. -o strmain.o strmain.cpp
strmain.cpp:13: warning: unused parameter ‘sig’
g++ -c -O2 -Wall -W -D_REENTRANT  -I../mortsrc -I../mortsrc/guilib -I../plugins -I../freelib -I. -o strbuff.o strbuff.cpp
g++ -c -O2 -Wall -W -D_REENTRANT  -I../mortsrc -I../mortsrc/guilib -I../plugins -I../freelib -I. -o plugins.o plugins.cpp
g++ -static-libgcc  -o sleap strmain.o   strbuff.o   plugins.o  ../freelib/readline/libreadline.a -lm ../plugins/libplugins.a ../mortsrc/libmort.a
cp -p sleap /home/userid/Documents/amber10/bin
make[2]: Leaving directory `/home/userid/Documents/amber10/src/gleap/leapsrc'
make[1]: Leaving directory `/home/userid/Documents/amber10/src/gleap'

Completed installation of AmberTools, version 1.1