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March 25, 2016July 21, 2017

OrthoDB 1.6 Installation On Ubuntu 14.04 (And Related) – Build Errors And The Simple Fixes

UPDATE: 20 May 2016 – With thanks to OrthoDB's very own Fredrik Tegenfeldt, here's a more distro-complete fix for the Makefile.rules file.

# BRH flags
ifeq ($(USE_BRH),1)
BRH_DIR        = $(BASE_DIR)
CPPFLAGS    += -I$(BRH_DIR)/src
ifeq ($(WITH_RPATH),1)
LDFLAGS        += -L$(LIB_DIR) -Wl,-rpath,$(LIB_INSTDIR)
else
LDFLAGS        += -L$(LIB_DIR)
endif
LDLIBS        += -lbrh
endif

ifeq ($(USE_BOOST_THREAD),1)
CPPFLAGS    += -pthread -DHAS_BOOST_THREADS
LDFLAGS        += -pthread
LDLIBS      += -L$(DIR_BOOST_LIB) -lboost_system -L$(DIR_BOOST_THREAD) -l$(LIB_BOOST_THREAD) -lpthread
endif

And Happy New Year,

Yet another random Ubuntu-centric bioinformatics aside in the event others run into the same build issues (with errors included below, as you likely googled those first). For those wondering…

The Hierarchical Catalog of Orthologs v8

Orthology (website, download) is the cornerstone of comparative genomics and gene function prediction. OrthoDB aims to classify protein-coding genes from the increasing number of available sequenced genomes into groups of orthologs descended from a single gene of the last common ancestor (LCA) of each clade of species. Applying this concept to the hierarchy of LCAs along the species phylogeny results in multiple levels of orthology: the more closely-related the species, the more finely-resolved the orthologous relations.

The build here was on a fresh installation of 64-bit Ubuntu 14.04 (Trusty Tahr). All of the errors produced come from running on that clean install, meaning you'll run into dumb errors (like missing build-essential), didn't-know-we-needed-that errors (boost), and that's-probbly-an-Ubuntu-oddity errors (with a modified Makefile.rules file with explicit boost calls linked to below; I suspect the developers are working on a non-Ubuntu distro).

Relevant apt-get's

sudo apt-get install build-essential libboost-all-dev

Relevant Downloads

* tclap (1.2.1) – tclap.sourceforge.net/

Stage 1 – Just Trying The Easy Install

I build everything in /opt by default and propose you do the same (whatever). First steps included.

username@ubuntu:~$ cd Downloads/
username@ubuntu:~/Downloads$ sudo mv OrthoDB_soft_1.6.tgz /opt/
username@ubuntu:~/Downloads$ cd /opt/
username@ubuntu:/opt$ sudo tar xvf OrthoDB_soft_1.6.tgz 

OrthoDB_soft_1.6/
OrthoDB_soft_1.6/BRHCLUS-1.12.7/
...
OrthoDB_soft_1.6/README
OrthoDB_soft_1.6/LICENSE

username@ubuntu:/opt$ cd OrthoDB_soft_1.6/
username@ubuntu:/opt/OrthoDB_soft_1.6$ sudo make WITH_RPATH=1 prefix=$(pwd) all
make: *** No rule to make target `all'.  Stop.

If you read the README file, you figure out to move to the BRHCLUS folder, then discover the need for the boost libraries, available via an apt-get:

username@ubuntu:/opt/OrthoDB_soft_1.6$ cd BRHCLUS-1.12.7/
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo ./configure.sh 
FATAL: cannot find boost libraries!
- Is boost installed (boost_system) ?
- Is boost installed in any of the search paths ?
  If not, add the path to PATH_SEARCH_LIB at the top of this script.

Stage 2 – sudo apt-get install libboost-all-dev

username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo apt-get install libboost-all-dev 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  account-plugin-windows-live libupstart1
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
  icu-devtools libboost-atomic-dev libboost-atomic1.54-dev
  libboost-atomic1.54.0 libboost-chrono-dev libboost-chrono1.54-dev
...
  libxml2-dev mpi-default-bin mpi-default-dev ocl-icd-libopencl1 openmpi-bin
  openmpi-common zlib1g-dev
0 upgraded, 102 newly installed, 0 to remove and 14 not upgraded.
Need to get 46.7 MB of archives.
After this operation, 262 MB of additional disk space will be used.
Do you want to continue? [Y/n] 
Get:1 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main libboost-atomic1.54.0 amd64 1.54.0-4ubuntu3.1 [8,076 B]
Get:2 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main libboost-chrono1.54.0 amd64 1.54.0-4ubuntu3.1 [12.5 kB]
Get:3 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/universe libboost-context1.54.0 amd64 1.54.0-4ubuntu3.1 [8,028 B]
Get:4 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main libboost-filesystem1.54.0 amd64 1.54.0-4ubuntu3.1 [34.2 kB]
...
Setting up libboost-wave-dev:amd64 (1.54.0.1ubuntu1) ...
Setting up libboost-all-dev (1.54.0.1ubuntu1) ...
Setting up libhwloc-plugins (1.8-1ubuntu1.14.04.1) ...
Processing triggers for libc-bin (2.19-0ubuntu6.6) ...

The configure stage now works…

username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo ./configure.sh 
OK - boost libraries
OK - boost thread libraries
OK - boost include dir
OK - tclap include dir
OK - thread pool include dir
Config file (/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/Makefile.config) successfully created

But, right off the bat, a clean install is missing build tools.

username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make WITH_RPATH=1 prefix=$(pwd) all
  Compiling brh_version.cpp
/bin/sh: 1: g++: not found
make[2]: *** [.linux/brh_version.o] Error 127
make[1]: *** [src] Error 2
make: *** [all] Error 2

Stage 3 – sudo apt-get install build-essential

username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo apt-get install build-essential 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  account-plugin-windows-live libupstart1
...
0 upgraded, 9 newly installed, 0 to remove and 14 not upgraded.
Need to get 15.9 MB of archives.
After this operation, 27.9 MB of additional disk space will be used.
Do you want to continue? [Y/n] 
Get:1 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main g++-4.8 amd64 4.8.4-2ubuntu1~14.04 [15.0 MB]
Get:2 http://us.archive.ubuntu.com/ubuntu/ trusty/main g++ amd64 4:4.8.2-1ubuntu6 [1,490 B]
Get:3 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main dpkg-dev all 1.17.5ubuntu5.5 [726 kB]
Get:4 http://us.archive.ubuntu.com/ubuntu/ trusty/main build-essential amd64 11.6ubuntu6 [4,838 B]
...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
Setting up libalgorithm-diff-perl (1.19.02-3) ...
Setting up libalgorithm-diff-xs-perl (0.04-2build4) ...
Setting up libalgorithm-merge-perl (0.08-2) ...

And the build process now takes steps forward.

username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make WITH_RPATH=1 prefix=$(pwd) all
  Compiling brh_version.cpp
  Compiling brh_common.cpp
  Compiling pairdataset.cpp
  Compiling brh_functions.cpp
  Compiling keymap.cpp
  Compiling inparalog.cpp
  Compiling clusterdata.cpp
  Compiling cluster.cpp
  Compiling clusterize.cpp
  Compiling cluster_functions.cpp
  Compiling modularity.cpp
  Compiling tri4algo.cpp
  Linking libbrh.so
  Compiling brhclus.cpp
  Linking brhclus
.linux/brhclus.o: In function `__static_initialization_and_destruction_0':
/usr/include/boost/system/error_code.hpp:222: undefined reference to `boost::system::generic_category()'
/usr/include/boost/system/error_code.hpp:223: undefined reference to `boost::system::generic_category()'
/usr/include/boost/system/error_code.hpp:224: undefined reference to `boost::system::system_category()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::detail::get_current_thread_data()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::disable_interruption::disable_interruption()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::interruption_point()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::start_thread_noexcept()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::interrupt()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::hiden::sleep_until(timespec const&)'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::join_noexcept()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `vtable for boost::detail::thread_data_base'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::native_handle()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::detach()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::disable_interruption::~disable_interruption()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `typeinfo for boost::detail::thread_data_base'
collect2: error: ld returned 1 exit status
make[2]: *** [/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/bin/brhclus] Error 1
make[1]: *** [tools/brhclus] Error 2
make: *** [all] Error 2

Stage 4 – tclap Install

A quick google search produces the following from info.circ.rochester.edu/BlueHive/Software/Bioinformatics/orthodb.html indicating that tclap is an OrthoDB dependency that needs to be satisfied. The version I've built below (1.2.1) can be downloaded from tclap.sourceforge.net

username@ubuntu:/opt$ ls
OrthoDB_soft_1.6  OrthoDB_soft_1.6.tgz  tclap-1.2.1.tar.gz

Extract and expand.

username@ubuntu:/opt$ sudo tar xvf tclap-1.2.1.tar.gz 
tclap-1.2.1/
tclap-1.2.1/aclocal.m4
tclap-1.2.1/AUTHORS
tclap-1.2.1/ChangeLog
...
tclap-1.2.1/config/Makefile.am
tclap-1.2.1/config/Makefile.in
tclap-1.2.1/config/missing
tclap-1.2.1/config/mkinstalldirs

The build process goes without issue.

username@ubuntu:/opt$ cd tclap-1.2.1/
username@ubuntu:/opt/tclap-1.2.1$ sudo ./configure 
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
...
config.status: creating tests/Makefile
config.status: creating config/config.h
config.status: executing depfiles commands
config.status: executing default commands

Onto make…

username@ubuntu:/opt/tclap-1.2.1$ sudo make
Making all in include
make[1]: Entering directory `/opt/tclap-1.2.1/include'
Making all in tclap
make[2]: Entering directory `/opt/tclap-1.2.1/include/tclap'
make[2]: Nothing to be done for `all'.
...
make[1]: Leaving directory `/opt/tclap-1.2.1/config'
make[1]: Entering directory `/opt/tclap-1.2.1'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory `/opt/tclap-1.2.1'

And make install…

username@ubuntu:/opt/tclap-1.2.1$ sudo make install
Making install in include
make[1]: Entering directory `/opt/tclap-1.2.1/include'
Making install in tclap
make[2]: Entering directory `/opt/tclap-1.2.1/include/tclap'
...
test -z "/usr/local/lib/pkgconfig" || /bin/mkdir -p "/usr/local/lib/pkgconfig"
 /usr/bin/install -c -m 644 'tclap.pc' '/usr/local/lib/pkgconfig/tclap.pc'
make[2]: Leaving directory `/opt/tclap-1.2.1'
make[1]: Leaving directory `/opt/tclap-1.2.1'

Stage 5 – Re-attempt The OrthoDB Build

The configure goes without issue again…

username@ubuntu:/opt$ cd OrthoDB_soft_1.6/
username@ubuntu:/opt/OrthoDB_soft_1.6$ cd BRHCLUS-1.12.7/
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make clean
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo ./configure.sh 
OK - boost libraries
OK - boost thread libraries
OK - boost include dir
OK - tclap include dir
OK - thread pool include dir
Config file (/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/Makefile.config) successfully created

But there's still an error at the make stage.

username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make all
  Compiling brh_version.cpp
  Compiling brh_common.cpp
  Compiling pairdataset.cpp
  Compiling brh_functions.cpp
  Compiling keymap.cpp
  Compiling inparalog.cpp
  Compiling clusterdata.cpp
  Compiling cluster.cpp
  Compiling clusterize.cpp
  Compiling cluster_functions.cpp
  Compiling modularity.cpp
  Compiling tri4algo.cpp
  Linking libbrh.so
  Compiling brhclus.cpp
  Linking brhclus
.linux/brhclus.o: In function `__static_initialization_and_destruction_0':
/usr/include/boost/system/error_code.hpp:222: undefined reference to `boost::system::generic_category()'
/usr/include/boost/system/error_code.hpp:223: undefined reference to `boost::system::generic_category()'
/usr/include/boost/system/error_code.hpp:224: undefined reference to `boost::system::system_category()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::detail::get_current_thread_data()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::disable_interruption::disable_interruption()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::interruption_point()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::start_thread_noexcept()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::interrupt()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::hiden::sleep_until(timespec const&)'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::join_noexcept()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `vtable for boost::detail::thread_data_base'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::native_handle()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::detach()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::disable_interruption::~disable_interruption()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `typeinfo for boost::detail::thread_data_base'
collect2: error: ld returned 1 exit status
make[2]: *** [/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/bin/brhclus] Error 1
make[1]: *** [tools/brhclus] Error 2
make: *** [all] Error 2

Stage 6 – Google Says Make Some Symbolic Links

A first fix for the boost error was to make symbolic links for libboost_thread.so and libboost_timer.so in /usr/lib.

username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ cd /usr/lib/x86_64-linux-gnu/
username@ubuntu:/usr/lib/x86_64-linux-gnu$ sudo ln -s libboost_thread.so /usr/lib
username@ubuntu:/usr/lib/x86_64-linux-gnu$ sudo ln -s libboost_timer.so /usr/lib
username@ubuntu:/usr/lib/x86_64-linux-gnu$ cd /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make clean
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo ./configure.sh 
OK - boost libraries
OK - boost thread libraries
OK - boost include dir
OK - tclap include dir
OK - thread pool include dir
Config file (/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/Makefile.config) successfully created

But this didn't work either.

username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make all
  Compiling brh_version.cpp
  Compiling brh_common.cpp
  Compiling pairdataset.cpp
  Compiling brh_functions.cpp
  Compiling keymap.cpp
  Compiling inparalog.cpp
  Compiling clusterdata.cpp
  Compiling cluster.cpp
  Compiling clusterize.cpp
  Compiling cluster_functions.cpp
  Compiling modularity.cpp
  Compiling tri4algo.cpp
  Linking libbrh.so
  Compiling brhclus.cpp
  Linking brhclus
.linux/brhclus.o: In function `__static_initialization_and_destruction_0':
/usr/include/boost/system/error_code.hpp:222: undefined reference to `boost::system::generic_category()'
/usr/include/boost/system/error_code.hpp:223: undefined reference to `boost::system::generic_category()'
/usr/include/boost/system/error_code.hpp:224: undefined reference to `boost::system::system_category()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::detail::get_current_thread_data()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::disable_interruption::disable_interruption()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::interruption_point()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::start_thread_noexcept()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::interrupt()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::hiden::sleep_until(timespec const&)'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::join_noexcept()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `vtable for boost::detail::thread_data_base'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::native_handle()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::thread::detach()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `boost::this_thread::disable_interruption::~disable_interruption()'
/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib/libbrh.so: undefined reference to `typeinfo for boost::detail::thread_data_base'
collect2: error: ld returned 1 exit status
make[2]: *** [/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/bin/brhclus] Error 1
make[1]: *** [tools/brhclus] Error 2
make: *** [all] Error 2

Stage 7 – The Boost Issue May Be Ubuntu-Specific

The final solution was to modify the Makefile.rules file to explicitly call on boost in Ubuntu. Make a backup copy of the Makefile.rules in the OrthoDB folder, then place this new Makefile.rules file into the same folder. The modified Makefile.rules is below for copy+paste, else you can download it here: 2016mar25_orthodb_Makefile_rules.txt (just rename the file and place into OrthoDB_soft_1.6/BRHCLUS-1.12.7).

username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo nano Makefile.rules

#
# Build rules
#

# Keep secondary files
.SECONDARY:

include $(ROOT_DIR)/Makefile.config
ifeq ($(strip $(DIR_TCLAP)),)
$(error "Build requires TCLAP package (http://tclap.sourceforge.net)")
endif

# if install, read build details
ifeq "$(MAKE-TARGET)" "install"
include $(ROOT_DIR)/.makefile.build
endif

# Object directory
OBJ_DIR		= .linux

# Use gcc4
CXX		= g++

# Use rpath or not
WITH_RPATH	?= 1

LDFLAGS		= 
ifeq "$(MAKE-TARGET)" "static"
WITH_RPATH	= 0
LDFLAGS		+= -static -lboost_system -lboost_thread -lpthread
endif

# check BOOST
USE_BOOST ?= 1

# check boost threads
USE_BOOST_THREAD ?= 1

ifeq ($(strip $(LIB_BOOST_THREAD)),)
USE_BOOST_THREAD = 0
USE_THREADPOOL = 0
endif

ifeq ($(strip $(DIR_THREADPOOL)),)
USE_THREADPOOL = 0
endif

# Library and binary directories
BASE_DIR	:= $(shell cd $(ROOT_DIR) ; pwd)

# Install directories
# With rpath, enforce install dir same as build
# Without, use same as build as default
# prefix - install topdir
# libdir/bindir - install lib/bin
# BASE_DIR - build top dir
# LIB_DIR/BIN_DIR - build top dir
#
# with rpath :
#   build and install dirs are the same
#   default top is BASE_DIR
# else :
#   build is always under BASE_DIR
#   install under prefix (default BASE_DIR)
#
#ifeq ($(WITH_RPATH),1)
#prefix		?= $(BASE_DIR)
#libdir		= $(prefix)/lib
#bindir		= $(prefix)/bin
##LIB_DIR		:= $(shell mkdir -p $(libdir) ; cd $(libdir) ; pwd)
##BIN_DIR		:= $(shell mkdir -p $(bindir) ; cd $(bindir) ; pwd)
#LIB_DIR		:= $(libdir)
#BIN_DIR		:= $(bindir)
#else
#LIB_DIR		:= $(shell mkdir -p $(BASE_DIR)/lib ; cd $(BASE_DIR)/lib ; pwd)
#BIN_DIR		:= $(shell mkdir -p $(BASE_DIR)/bin ; cd $(BASE_DIR)/bin ; pwd)
#prefix		?= $(BASE_DIR)
#libdir		?= $(LIB_DIR)
#bindir		?= $(BIN_DIR)
#endif
LIB_DIR		:= $(shell mkdir -p $(BASE_DIR)/lib ; cd $(BASE_DIR)/lib ; pwd)
BIN_DIR		:= $(shell mkdir -p $(BASE_DIR)/bin ; cd $(BASE_DIR)/bin ; pwd)
prefix		?= $(BASE_DIR)
libdir		?= $(LIB_DIR)
bindir		?= $(BIN_DIR)
LIB_INSTDIR := $(prefix)/lib
BIN_INSTDIR := $(prefix)/bin

# Install user/group
INST_USR	 = $(shell whoami)
INST_GRP	?= $(shell groups | cut -f 1 -d ' ' )

# Establish install command
# if rpath -> always chown
# else
#   if targetdir==installdir -> chown
#   else install
# endif
#ifeq ($(WITH_RPATH),1)
#INST_CMD	 = chown $(INST_USR).$(INST_GRP)
#else
TARGET_DIR	= $(dir $(TARGET))
rpTARGET	= $(realpath $(firstword $(TARGET_DIR)))
rpINSTDIR	= $(realpath $(prefix)/$(INSTDIR))
ifeq ($(rpTARGET),$(rpINSTDIR))
INST_CMD	 = chown $(INST_USR).$(INST_GRP)
else
INST_CMD	 = mkdir -p $(prefix)/$(INSTDIR); install -D -m 755 -g $(INST_GRP) -t $(prefix)/$(INSTDIR)
endif
#endif

# Definitions concerning build environment
CPPFLAGS	+= -DBRH_BUILD_ENV="\"$(shell uname -s -r -v -m -i -p -o)\""
CPPFLAGS	+= -DBRH_BUILD_TIME="\"$(shell date)\""

# Default pre-processor flags
CPPFLAGS	+= -DBASE_DIR="\"$(BASE_DIR)\""
CPPFLAGS	+= -D_REENTRANT
CPPFLAGS	+= -D_XOPEN_SOURCE

# c++ standard
CPPFLAGS	+= -std=c++11
CXXFLAGS	+= -std=c++11

# debug flag
ifeq ($(USE_DEBUG),3)
CXXFLAGS	+= -fno-inline -fbounds-check
else ifeq ($(USE_DEBUG),2)
CPPFLAGS	+= -DBRH_DEBUG
CXXFLAGS	+= -fno-inline -fbounds-check
else ifeq ($(USE_DEBUG),1)
CPPFLAGS	+= -DBRH_CHECK_IT
CXXFLAGS	+= -finline-functions -fbounds-check
else
CXXFLAGS	+= -finline-functions
endif

# Default compiler flags
CXXFLAGS	+= -fPIC
CXXFLAGS	+= -MMD
CXXFLAGS	+= -g
CXXFLAGS	+= -Wall -Werror
CXXFLAGS	+= -fexceptions
#CXXFLAGS	+= -fno-inline
CXXFLAGS	+= -O3
#CXXFLAGS	+= -O0
CXXFLAGS	+= -I$(BASE_DIR)/src
#CXXFLAGS	+= -std=c++11
#CXXFLAGS	+= -pg
#LDFLAGS		+= -pg

# BRH flags
ifeq ($(USE_BRH),1)
BRH_DIR		= $(BASE_DIR)
CPPFLAGS	+= -I$(BRH_DIR)/src
ifeq ($(WITH_RPATH),1)
LDFLAGS		+= -L$(LIB_DIR) -Wl,-rpath,$(LIB_INSTDIR) -lboost_system -lboost_thread -lpthread
else
LDFLAGS		+= -L$(LIB_DIR) -lboost_system -lboost_thread -lpthread
endif
LDLIBS		+= -lbrh -lboost_system -lboost_thread -lpthread
endif

ifeq ($(USE_BOOST_THREAD),1)
CPPFLAGS	+= -pthread -DHAS_BOOST_THREADS
LDFLAGS		+= -pthread -L$(DIR_BOOST_LIB) -lboost_system -lboost_thread -lpthread -L$(DIR_BOOST_THREAD) -l$(LIB_BOOST_THREAD)
endif

ifeq ($(USE_THREADPOOL),1)
CPPFLAGS	+= -DHAS_BOOST_THREADPOOL
CPPFLAGS	+= -I$(DIR_THREADPOOL)
endif

ifeq ($(USE_BOOST),1)
CPPFLAGS	+= -I$(DIR_BOOST_INC)
endif

# TCLAP flags
ifeq ($(USE_TCLAP),1)
CPPFLAGS	+= -I$(DIR_TCLAP)
endif

# BOOST flags
ifeq ($(USE_THREAD),1)
endif

# Check file type
ifeq ($(suffix $(firstword $(SOURCES))),.cpp)
IS_CPP		= 1
else
IS_CPP		= 0
endif

# List of objects
ifeq ($(IS_CPP),1)
OBJECTS		= $(SOURCES:%.cpp=$(OBJ_DIR)/%.o)
endif

# Default build
default:	all

ifeq ($(IS_CPP),1)
# Build a binary
$(BIN_DIR)/%: $(OBJECTS) Makefile $(BASE_DIR)/Makefile.rules
	@echo "  Linking $(@F)"
	@mkdir -p $(@D)
	@$(LINK.cc) $(LDFLAGS) -o $@ $(OBJECTS) $(LDLIBS)

# Build a shared library
$(LIB_DIR)/%.so: $(OBJECTS) Makefile $(BASE_DIR)/Makefile.rules
	@echo "  Linking $(@F)"
	@mkdir -p $(@D)
	@$(LINK.cc) -shared -o $@ $(OBJECTS) $(LDLIBS)

# Build a static library
$(LIB_DIR)/%.a: $(OBJECTS) Makefile $(BASE_DIR)/Makefile.rules
	@echo "  Linking $(@F)"
	@mkdir -p $(@D)
	@ar rcs $@ $(OBJECTS)

# Include dependency files
-include $(OBJECTS:%.o=%.d)

# Build an object file
$(OBJ_DIR)/%.o: %.cpp Makefile
	@echo "  Compiling $< "
	@mkdir -p $(@D)
	@$(COMPILE.cc) -o $@ $<
else
$(BIN_DIR)/%.py: %.py
	@echo "  Copying $< to target dir"
	@cp -f $< $@
endif



# Main targets are phony
.PHONY: default all clean_target clean_obj doc clean_doc clean install static

# Build target
all:	$(TARGET)

static:	$(TARGET)

# Clean objects
clean_obj:
	@$(RM) -r $(OBJ_DIR)

# Clean build
clean_target:
	@$(RM) -r $(OBJ_DIR) $(TARGET)

# Build documentation
doc:
	@$(MAKE) -C $(BASE_DIR) $@

# Clean build
clean: clean_target

# Install
install:
#	@echo "rpT   : $(rpTARGET)"
#	@echo "rpI   : $(rpINSTDIR)"
#	@echo "rpath : $(WITH_RPATH)"
#	@echo "inst  : $(INST_CMD) $(TARGET)"
	@target="$(TARGET)"; \
	[ $${#target} -gt 0 ] || target="$(OUTPUT)"; \
	for f in $${target}; do \
	    fname=`basename $$f`; \
	    if [ -f $$f ]; then \
	       echo "Installing in $(prefix)/$(INSTDIR)    <$$fname>"; \
	       $(INST_CMD) $$f; \
	    fi; \
	done

The configure step runs fine…

username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make clean
username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo ./configure.sh 
OK - boost libraries
OK - boost thread libraries
OK - boost include dir
OK - tclap include dir
OK - thread pool include dir
Config file (/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/Makefile.config) successfully created

…and the build itself runs fine.

username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make all
  Compiling brh_version.cpp
  Compiling brh_common.cpp
  Compiling pairdataset.cpp
  Compiling brh_functions.cpp
  Compiling keymap.cpp
  Compiling inparalog.cpp
  Compiling clusterdata.cpp
  Compiling cluster.cpp
  Compiling clusterize.cpp
  Compiling cluster_functions.cpp
  Compiling modularity.cpp
  Compiling tri4algo.cpp
  Linking libbrh.so
  Compiling brhclus.cpp
  Linking brhclus
  Compiling evolrate.cpp
  Linking evolrate
  Compiling statbrh.cpp
  Linking statbrh
  Compiling brh2x.cpp
  Linking brh2x
  Compiling statclus.cpp
  Linking statclus
  Compiling cmpclus.cpp
  Linking cmpclus
  Compiling getclus.cpp
  Linking getclus
  Compiling cmpbrh.cpp
  Linking cmpbrh
  Compiling cmpinpar.cpp
  Linking cmpinpar
  Compiling renumclus.cpp
  Linking renumclus
  Compiling getinpar.cpp
  Linking getinpar
  Compiling mergeinpar.cpp
  Linking mergeinpar
  Compiling align2brh.cpp
  Linking align2brh
  Compiling findbrh.cpp
  Linking findbrh
  Copying parsedump.py to target dir
  Copying getbrh.py to target dir
  Copying plot_brhclus_progress.py to target dir

Stage 8 – Build The Tests

Just to make sure all is working, make globaltest.

username@ubuntu:/opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7$ sudo make globaltest


-------------------------------------------------------------
Binary  dir : /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/bin
Library dir : /opt/OrthoDB_soft_1.6/BRHCLUS-1.12.7/lib
-------------------------------------------------------------

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TEST MACHINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uname [ Linux ubuntux 3.16.0-59-generic #79~14.04.1-Ubuntu SMP Mon Jan 18 15:41:27...]
cpu   [ Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz]
mem   [ MemTotal:        3949740 kB]

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TEST BRHCLUS
with option --single
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
------------------------------
run default setup
------------------------------
------------------------------
run with harder e-value cuts
------------------------------
------------------------------
run with soft e-value cuts
------------------------------
------------------------------
Check output files
------------------------------
default                                [OK]
hard_e-val                             [OK]
soft_e-val                             [OK]
------------------------------
Check timing
------------------------------
default                                [16 %]
hard_e-val                             [-8 %]
soft_e-val                             [10 %]

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TEST BRHCLUS, resume function
with option --single
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
resume                                 [OK, contents same but clids or seqs differ]

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TEST BRHCLUS
with option --nostringent
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
------------------------------
run default setup
------------------------------
------------------------------
run with harder e-value cuts
------------------------------
------------------------------
run with soft e-value cuts
------------------------------
------------------------------
Check output files
------------------------------
default                                [OK]
hard_e-val                             [OK]
soft_e-val                             [OK]
------------------------------
Check timing
------------------------------
default                                [18 %]
hard_e-val                             [10 %]
soft_e-val                             [2 %]

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TEST BRHCLUS, resume function
with option --nostringent
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
resume                                 [OK, contents same but clids or seqs differ]

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TEST BRHCLUS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
------------------------------
run default setup
------------------------------
------------------------------
run with harder e-value cuts
------------------------------
------------------------------
run with soft e-value cuts
------------------------------
------------------------------
Check output files
------------------------------
default                                [OK]
hard_e-val                             [OK]
soft_e-val                             [OK]
------------------------------
Check timing
------------------------------
default                                [7 %]
hard_e-val                             [8 %]
soft_e-val                             [12 %]

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TEST BRHCLUS, resume function
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
resume                                 [OK, contents same but clids or seqs differ]

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TEST BRHCLUS
with option --lowmem
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
------------------------------
run default setup
------------------------------
------------------------------
run with harder e-value cuts
------------------------------
------------------------------
run with soft e-value cuts
------------------------------
------------------------------
Check output files
------------------------------
default                                [OK]
hard_e-val                             [OK]
soft_e-val                             [OK]
------------------------------
Check timing
------------------------------
default                                [6 %]
hard_e-val                             [8 %]
soft_e-val                             [7 %]

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TEST BRHCLUS, resume function
with option --lowmem
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
resume                                 [OK, contents same but clids or seqs differ]

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TEST BRHCLUS
merge BRHs into an existing cluster configuration
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mergebrh                               [OK]

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TEST STATCLUS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
default                                [OK]
hard_e-val                             [OK]
soft_e-val                             [OK]

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TEST CMPCLUS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
exact_match                            [OK]
mis-match                              [OK]

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TEST CMPCLUS
related groups
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
default                                [OK]

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TEST MERGEINPAR
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
clusters                               [OK]
unresolved                             [OK]


------------------------------------------
Warnings (4) were detected.
------------------------------------------

Most likely this is of not concern and the probable origin are messages like

  [OK, contents same but clids or seqs differ]

They may be caused by rounding errors on different architectures/versions of the software.

April 5, 2014July 21, 2017

Compiling And Running GAMESS-US (1 May 2013(R1)) On 64-bit Ubuntu 12.X/13.X In SMP Mode

Author's Note 1: It is my standard policy to put too much info into guides so that those who are searching for specific problems they come across will find the offending text in their searches. With luck, your "build error" search sent you here.

Author's Note 2: It's not as bad as it looks (I've included lots of output and error messages for easy searching)!

Author's Note 3: I won't be much help for you in diagnosing your errors, but am happy to tweak the text below if something is unclear.

Conventions: I include both the commands you type in your Terminal and some of the output from these commands, the output being where most of the errors appear that I work on in the discussion.

Input is formatted as below:

username – your username (check your prompt)
machinename – your hostname (type hostname or check your prompt)

Text you put in at the (also shown, so you see the directory structure) prompt (copy + paste should be fine)

Text you get out (for checking results and reproducing errors)

Having just recently downloaded the newest version of GAMESS-US (R1 2013), my first few passes at using it under Linux (specifically, Ubuntu 12.04) ran into a few walls that required some straightforward modifications and a little bit of system prep planning. As my first few passes before successful execution are likely the same exact problems you might have run into in your attempts to get GAMESS-US to run (after a successful compilation and linking), I'm posting my problems and solutions here.

Qualifier 1 – My concern at the moment has been to get GAMESS-US to run under 64-bit Ubuntu 12.04 on a multi-core board (ye olde symmetric multiprocessing (which I always called single multi-processor, or SMP)). While some answers may follow in what's below, this post doesn't cover MPI-specific builds (nothing through a router, that is). SMP is the only concern (which is to say, I likely won't have good answers if you send along an MPI-specific question). Also, although I'm VERY interested in trying it, I've not yet attempted to build a GPU-capable version (but plan to in the near future).

Qualifier 2 – It is my standard policy to install apps into /opt, and my steps below will reflect that (specifically because there's a permission issue that needs to be addressed when you first try to build components). You can default to whatever you like, but keep in mind my tweaks when you try to build your local copy.

So, with the qualifiers in mind…

1. Prepping The System (apt-get)

There are few things better than being able to apt-get everything you need to prep your machine for an install, and I'm pleased to report that the (current) process for putting the important files onto Ubuntu 12.X/13.X is easy. Assuming you're not going the Intel / PGI / MKL route, you can do everything by installing gfortran (compiler, presently installing 4.4) and the blas and atlas math libraries.

username@machinename:~$ sudo apt-get install gfortran libblas-dev libatlas-base-dev

Note: your atlas libraries will be installed in /usr/lib64/atlas/ – this will matter when you run config.

After these finish, run the following to determine your installed gfortran version (will be asked for by the new GAMESS config)

username@machinename:~$ gfortran -dumpversion

GNU Fortran (Ubuntu 4.4.3-4ubuntu5.1) 4.4.3
Copyright (C) 2010 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING

4.4 And you're ready for GAMESS.

2. Downloading GAMESS-US, Placing Into /opt, And Changing Permissions

First, obviously, get the GAMESS source (click on the red text).

After downloading, copy/move gamess-current.tar.gz into /opt

username@machinename:~$ cd ~/Downloads
username@machinename:~/Downloads$ sudo cp gamess-current.tar.gz /opt
username@machinename:~/Downloads$ cd /opt
username@machinename:/opt$ sudo gunzip gamess-cuerent.tar.gz
username@machinename:/opt$ sudo tar xvd gamess-current.tar

gamess/
gamess/gms-files.csh
gamess/tools/
…
gamess/misc/count.code
gamess/misc/vbdum.src
gamess/Makefile.in

At this point, if you go through the config process and get to the point of building ddikick.x, you will get an error when you first try to run ./compddi

username@machinename:/opt/gamess/ddi$ sudo ./compddi >& compddi.log &

[1] 4622
-bash: compddi.log: Permission denied

The problem is with the permission of the entire gamess folder:

drwxr-xr-x  4 root        root              4096 2014-04-04 21:43 .
drwxr-xr-x 22 root        root              4096 2013-12-27 16:17 ..
drwxr-xr-x 14 1300 504              4096 2014-04-04 21:43 gamess
-rw-r–r– 1 root        root         198481920 2014-04-04 21:42 gamess-current.tar

Which you remedy before running into this error by changing the permissions:

username@machinename:/opt$ sudo chown -R username gamess

The next step is recommended when you run config, so I'm performing the step here to get it out of the way. With the atlas libraries installed, generate two symbolic links.

username@machinename:/opt$ cd /usr/lib64/atlas
username@machinename:/usr/lib64/atlas$ sudo ln -s libf77blas.so.3.0 libf77blas.so
username@machinename:/usr/lib64/atlas$ sudo ln -s libatlas.so.3.0 libatlas.so

And, at this point, you're ready to run the new (well, new to me) config script that preps your system install.

3. Building GAMESS-US

Back to the GAMESS-US folder.

username@machinename:/usr/lib64/atlas$ cd /opt/gamess
username@machinename:/opt/gamess$ sudo ./config

This script asks a few questions, depending on your computer system,
to set up compiler names, libraries, message passing libraries,
and so forth.

You can quit at any time by pressing control-C, and then .

Please open a second window by logging into your target machine,
in case this script asks you to 'type' a command to learn something
about your system software situation. All such extra questions will
use the word 'type' to indicate it is a command for the other window.

After the new window is open, please hit to go on.

You can open that second window or blindly assume that what I include below is all you need.

[enter]

GAMESS can compile on the following 32 bit or 64 bit machines:
axp64 – Alpha chip, native compiler, running Tru64 or Linux
cray-xt – Cray's massively parallel system, running CNL
hpux32 – HP PA-RISC chips (old models only), running HP-UX
hpux64 – HP Intel or PA-RISC chips, running HP-UX
ibm32 – IBM (old models only), running AIX
ibm64 – IBM, Power3 chip or newer, running AIX or Linux
ibm64-sp – IBM SP parallel system, running AIX
ibm-bg – IBM Blue Gene (P or L model), these are 32 bit systems
linux32 – Linux (any 32 bit distribution), for x86 (old systems only)
linux64 – Linux (any 64 bit distribution), for x86_64 or ia64 chips
AMD/Intel chip Linux machines are sold by many companies
mac32 – Apple Mac, any chip, running OS X 10.4 or older
mac64 – Apple Mac, any chip, running OS X 10.5 or newer
sgi32 – Silicon Graphics Inc., MIPS chip only, running Irix
sgi64 – Silicon Graphics Inc., MIPS chip only, running Irix
sun32 – Sun ultraSPARC chips (old models only), running Solaris
sun64 – Sun ultraSPARC or Opteron chips, running Solaris
win32 – Windows 32-bit (Windows XP, Vista, 7, Compute Cluster, HPC Edition)
win64 – Windows 64-bit (Windows XP, Vista, 7, Compute Cluster, HPC Edition)
winazure – Windows Azure Cloud Platform running Windows 64-bit
type 'uname -a' to partially clarify your computer's flavor.
please enter your target machine name:

We're doing a linux64 build, so type the following at the prompt:

linux64

Where is the GAMESS software on your system?
A typical response might be /u1/mike/gamess,
most probably the correct answer is /opt/gamess

GAMESS directory? [/opt/gamess]

Who is this mike and where is my folder u1? We'll get to that in rungms. For now, I'm installing in /opt, so the default directory is fine:

[enter]

Setting up GAMESS compile and link for GMS_TARGET=linux64
GAMESS software is located at GMS_PATH=/opt/gamess

Please provide the name of the build locaation.
This may be the same location as the GAMESS directory.

GAMESS build directory? [/opt/gamess]

Fine as selected.

[enter]

Please provide a version number for the GAMESS executable.
This will be used as the middle part of the binary's name,
for example: gamess.00.x

Version? [00]

Is this important? Maybe, if you plan on building multiple versions of GAMESS-US (you might want a GPU-friendly version, one with a different compiler, one with MPI, etc.). Number as you wish and remember the number when it comes to rungms. That said, the actual linking step seems to really want to produce a 01 version (we'll get to that). Meantime, default value is fine.

[enter]

Linux offers many choices for FORTRAN compilers, including the GNU
compiler set ('g77' in old versions of Linux, or 'gfortran' in
current versions), which are included for free in Unix distributions.

There are also commercial compilers, namely Intel's 'ifort',
Portland Group's 'pgfortran', and Pathscale's 'pathf90'. The last
two are not common, and aren't as well tested as the others.

type 'rpm -aq | grep gcc' to check on all GNU compilers, including gcc
type 'which gfortran' to look for GNU's gfortran (a very good choice),
type 'which g77' to look for GNU's g77,
type 'which ifort' to look for Intel's compiler,
type 'which pgfortran' to look for Portland Group's compiler,
type 'which pathf90' to look for Pathscale's compiler.
Please enter your choice of FORTRAN:

We're using gfortran (currently 4.4.3):

gfortran

gfortran is very robust, so this is a wise choice.

Please type 'gfortran -dumpversion' or else 'gfortran -v' to
detect the version number of your gfortran.
This reply should be a string with at least two decimal points,
such as 4.1.2 or 4.6.1, or maybe even 4.4.2-12.
The reply may be labeled as a 'gcc' version,
but it is really your gfortran version.
Please enter only the first decimal place, such as 4.1 or 4.6:

4.4

Alas, your version of gfortran does not support REAL*16,
so relativistic integrals cannot use quadruple precision.
Other than this, everything will work properly.
hit to continue to the math library setup.

If this was my biggest concern I'd be a happy quantum chemist. Obviously you can try to install other flavors of gfortran and, possibly, by the time you need the procedure I'm following, a newer version of gfortran will be apt-gotten.

[enter]

Linux distributions do not include a standard math library.

There are several reasonable add-on library choices,
MKL from Intel for 32 or 64 bit Linux (very fast)
ACML from AMD for 32 or 64 bit Linux (free)
ATLAS from www.rpmfind.net for 32 or 64 bit Linux (free)
and one very unreasonable option, namely 'none', which will use
some slow FORTRAN routines supplied with GAMESS. Choosing 'none'
will run MP2 jobs 2x slower, or CCSD(T) jobs 5x slower.

Some typical places (but not the only ones) to find math libraries are
Type 'ls /opt/intel/mkl' to look for MKL
Type 'ls /opt/intel/Compiler/mkl' to look for MKL
Type 'ls /opt/intel/composerxe/mkl' to look for MKL
Type 'ls -d /opt/acml*' to look for ACML
Type 'ls -d /usr/local/acml*' to look for ACML
Type 'ls /usr/lib64/atlas' to look for Atlas

Enter your choice of 'mkl' or 'atlas' or 'acml' or 'none':

atlas

Where is your Atlas math library installed? A likely place is
/usr/lib64/atlas
Please enter the Atlas subdirectory on your system:

Our location is, in fact, /usr/lib64/atlas, so we type it in accordingly.

NOTE: If you don't type anything but [enter] below, the script closes (/usr/lib64/atlas is listed as the expected location, but it is not defaulted by the script. You need to type it in.

/usr/lib64/atlas

The linking step in GAMESS assumes that a softlink exists
within the system's /usr/lib64/atlas
from libatlas.so to a specific file like libatlas.so.3.0
from libf77blas.so to a specific file like libf77blas.so.3.0
config can carry on for the moment, but the 'root' user should
chdir /usr/lib64/atlas
ln -s libf77blas.so.3.0 libf77blas.so
ln -s libatlas.so.3.0 libatlas.so
prior to the linking of GAMESS to a binary executable.

Math library 'atlas' will be taken from /usr/lib64/atlas

please hit to compile the GAMESS source code activator

The symbolic linking was performed before the GAMESS steps.

[enter]

gfortran -o /home/username/gamess/tools/actvte.x actvte.f
unset echo
Source code activator was successfully compiled.

please hit to set up your network for Linux clusters.

[enter]

If you have a slow network, like Gigabit Ethernet (GE), or
if you have so few nodes you won't run extensively in parallel, or
if you have no MPI library installed, or
if you want a fail-safe compile/link and easy execution,
choose 'sockets'
to use good old reliable standard TCP/IP networking.

If you have an expensive but fast network like Infiniband (IB), and
if you have an MPI library correctly installed,
choose 'mpi'.

communication library ('sockets' or 'mpi')?

Again, I'm not building an mpi-friendly version, so am using sockets.

sockets

64 bit Linux builds can attach a special LIBCCHEM code for fast
MP2 and CCSD(T) runs. The LIBCCHEM code can utilize nVIDIA GPUs,
through the CUDA libraries, if GPUs are available.
Usage of LIBCCHEM requires installation of HDF5 I/O software as well.
GAMESS+LIBCCHEM binaries are unable to run most of GAMESS computations,
and are a bit harder to create due to the additional CUDA/HDF5 software.
Therefore, the first time you run 'config', the best answer is 'no'!
If you decide to try LIBCCHEM later, just run this 'config' again.

Do you want to try LIBCCHEM? (yes/no):

no

Your configuration for GAMESS compilation is now in
/home/username/gamess/install.info
Now, please follow the directions in
/home/username/gamess/machines/readme.unix
username@machinename:~/gamess$

At this stage, you're ready to build ddikick.x and continue with the compiling.

4. Build ddikick.x

username@machinename:/opt/gamess$ cd ddi
username@machinename:/opt/gamess/ddi$ sudo ./compddi >& compddi.log &

Will dump output into compddi.log (which will now work with the correct permissions).

username@machinename:/opt/gamess/ddi$ sudo mv ddikick.x ..
username@machinename:/opt/gamess/ddi$ cd ..
username@machinename:/opt/gamess$ sudo ./compall >& compall.log &

Feel free to follow along as compall.log dumps results. You're also welcome to follow the readme.unix advice:

This takes a while, so go for coffee, or check the SF Giants web page.

Upon completion, the last step is to link the executable.

Now, it used to be the case that you specified the version number in the lked step. So, if you wanted to stick with the 00 version from the config file, you'd type

username@machinename:/opt/gamess$ sudo ./lked gamess 00 >& lked.log &

When you do that at present, you get

[1] 7626
username@machinename:/opt/gamess$

[1]+ Stopped sudo ./lked gamess 00 &>lked.log

This then leads you to use the lked call from the readme.unix file.

username@machinename:/opt/gamess$ sudo ./lked gamess 01 >& lked.log &

Which then produces lked.log and gamess.01.x.

Now, if you run with 00 again, you get a successful linking of gamess.00.x . Not sure why this happens, but the version number isn't important so long as you specify the right one when you use rungms (so I've not diagnosed it further).

At this point, you have a gamess.00.x and/or gamess.01.x executable in your /opt/gamess folder:

30828747 2014-04-04 22:41 gamess.01.x

I'm going to ignore the 00 issue out of the config file and use the gamess.01.x executable.

We're ready to run calculations and work through the next set of errors you'll receive if you don't properly modify files.

5. PATH Setting

First, we copy rungms to our home folder, then add /opt/gamess to the PATH:

username@machinename:/opt/gamess$ cp rungms ~/
username@machinename:/opt/gamess$ cd ~/
username@machinename:~$ nano .bashrc

Add the following to the bottom of .bashrc (or extend your PATH)

PATH=$PATH:/opt/gamess

Quit nano and source.

username@machinename:~$ source .bashrc
[OPTIONAL] username@machinename:~$ echo $PATH

/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:…/opt/gamess:

6. rungms (Probably Why You're Here)

If you just go blindly into a run, you'll get the following error:

username@machinename:~$ ./rungms test.inp

—– GAMESS execution script 'rungms' —–
This job is running on host machinename
under operating system Linux at Fri Apr 4 22:47:55 EDT 2014
Available scratch disk space (Kbyte units) at beginning of the job is
df: `/scr/username': No such file or directory
df: no file systems processed
GAMESS temporary binary files will be written to /scr/username
GAMESS supplementary output files will be written to /home/username/scr
Copying input file test.inp to your run's scratch directory…
cp test.inp /scr/username/test.F05
cp: cannot create regular file `/scr/username/test.F05': No such file or directory
unset echo
/u1/mike/gamess/gms-files.csh: No such file or directory.

As is obvious, rungms needs some modifying.

username@machinename:~$ nano rungms

Scroll down until you see the following:

set TARGET=sockets
set SCR=/scr/$USER
set USERSCR=~$USER/scr
set GMSPATH=/u1/mike/gamess

Given that it's just me on the machine, I tend to simplify this by making SCR and USERSCR the same directory, and I make them both /tmp. If you intend on keeping all of the files, you'll need to make rungms specific for each run case. My only concerns are .dat and .log, so /tmp dumping is fine. Furthermore, we must change GMSPATH from how the ever-helpful Mike Schmidt (he got me through some early issues when I started my GAMESS-US adventure 15ish years ago. Won't complain about his continued default-ed presence in the scripts) has it set up at Iowa to how we want it on our own machines (in my case, /opt/gamess)

set TARGET=sockets
set SCR=/tmp
set USERSCR=/tmp
set GMSPATH=/opt/gamess

With these modifications, your next run will be a bit more successful:

username@machinename:~$ ./rungms test.inp

—– GAMESS execution script 'rungms' —–
This job is running on host machinename
under operating system Linux at Fri Apr 4 22:51:35 EDT 2014
Available scratch disk space (Kbyte units) at beginning of the job is
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/sda2 1905222596 249225412 1559217460 14% /
GAMESS temporary binary files will be written to /tmp
GAMESS supplementary output files will be written to /tmp
Copying input file test.inp to your run's scratch directory…
cp test.inp /tmp/test.F05
unset echo
/opt/gamess/ddikick.x /opt/gamess/gamess.00.x test -ddi 1 1 machinename -scr /tmp

Distributed Data Interface kickoff program.
Initiating 1 compute processes on 1 nodes to run the following command:
/opt/gamess/gamess.00.x test

******************************************************
* GAMESS VERSION = 1 MAY 2013 (R1) *
* FROM IOWA STATE UNIVERSITY *
* M.W.SCHMIDT, K.K.BALDRIDGE, J.A.BOATZ, S.T.ELBERT, *
* M.S.GORDON, J.H.JENSEN, S.KOSEKI, N.MATSUNAGA, *
* K.A.NGUYEN, S.J.SU, T.L.WINDUS, *
* TOGETHER WITH M.DUPUIS, J.A.MONTGOMERY *
* J.COMPUT.CHEM. 14, 1347-1363(1993) *
**************** 64 BIT LINUX VERSION ****************
…
INPUT CARD>
DDI Process 0: shmget returned an error.
Error EINVAL: Attempting to create 160525768 bytes of shared memory.
Check system limits on the size of SysV shared memory segments.

The file ~/gamess/ddi/readme.ddi contains information on how to display
the current SystemV memory settings, and how to increase their sizes.
Increasing the setting requires the root password, and usually a sytem reboot.

DDI Process 0: error code 911
ddikick.x: application process 0 quit unexpectedly.
ddikick.x: Fatal error detected.
The error is most likely to be in the application, so check for
input errors, disk space, memory needs, application bugs, etc.
ddikick.x will now clean up all processes, and exit…
ddikick.x: Sending kill signal to DDI processes.
ddikick.x: Execution terminated due to error(s).
unset echo
—– accounting info —–
Files used on the master node machinename were:
-rw-r–r– 1 username username 0 2014-04-04 22:51 /tmp/test.dat
-rw-r–r– 1 username username 1341 2014-04-04 22:51 /tmp/test.F05
ls: No match.
ls: No match.
ls: No match.
Fri Apr 4 22:51:36 EDT 2014
0.0u 0.0s 0:01.08 9.2% 0+0k 0+8io 0pf+0w

Things worked, but with a memory error. This issue is discussed at the Baldridge Group wiki: ocikbapps.uzh.ch/kbwiki/gamess_troubleshooting.html

From the wiki:

If you are sure you are not asking for too much memory in the input file, check that your kernel parameters are not allowing enough memory to be requested. You might have to increase the SHMALL & SHMAX kernel memory values to allow GAMESS to run. (See http://www.pythian.com/news/245/the-mysterious-world-of-shmmax-and-shmall/ for a better explanation.)
For example, on a machine with 4GB of memory, you might add these to /etc/sysctl.conf:
# cat /etc/sysctl.conf | grep shm
kernel.shmmax = 3064372224
kernel.shmall = 748137
Then set the new settings like so:
# sysctl -p
Since they are in /etc/sysctl.conf, they will automatically be set each time the system is booted.

In our case, we modify sysctl.conf with the recommendations from the wiki:

username@machinename:~$ sudo nano /etc/sysctl.conf

Add the following to the bottom of the file:

kernel.shmmax = 3064372224
kernel.shmall = 748137

Save and exit.

username@machinename:~$ sudo sysctl -p

net.ipv4.ip_forward = 1
kernel.shmmax = 3064372224
kernel.shmall = 748137

These memory values will change depending on your system.

Now we empty the /tmp and rerun.

username@machinename:~$ rm /tmp/*
username@machinename:~$ ./rungms test.inp

If your input file is worth it's salt, you'll have successfully run your file on a single processor (single core, that is). If you run into additional memory errors, increase kernel.shmmax and kernel.shmall.

Now, onto the SMP part. My first attempt to run games in parallel (on 4 cores using version 00) produced the following error:

username@machinename:~$ rm /tmp/*
username@machinename:~$ ./rungms test.inp 00 4

—– GAMESS execution script 'rungms' —–
This job is running on host machinename
under operating system Linux at Fri Apr 4 22:52:52 EDT 2014
Available scratch disk space (Kbyte units) at beginning of the job is
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/sda2 1905222596 249225416 1559217456 14% /
GAMESS temporary binary files will be written to /tmp
GAMESS supplementary output files will be written to /tmp
Copying input file test.inp to your run's scratch directory…
cp test.inp /tmp/test.F05
unset echo
I do not know how to run this node in parallel.

I tried a number of stupid things to get the run to work, finally settling on modifying the rungms file properly. To make gamess know how to run the node in parallel, we need only make the following changes to our rungms file.

username@machinename:~$ nano rungms

Scroll down until you find the section below:

# 2. This is an example of how to run on a multi-core SMP enclosure,
# where all CPUs (aka COREs) are inside a -single- NODE.
# At other locations, you may wish to consider some of the examples
# that follow below, after commenting out this ISU specific part.
if ($NCPUS > 1) then
switch (`hostname`)
case se.msg.chem.iastate.edu:
case sb.msg.chem.iastate.edu:
if ($NCPUS > 2) set NCPUS=4
set NNODES=1

The change is simple. We remove the cases for $NCPUS > 1 in the file and add the hostname of our linux box (and if you don't know this or it's not in your prompt, simply type hostname at the prompt first). We'll disable the two cases listed and add our hostname to the case list.

# 2. This is an example of how to run on a multi-core SMP enclosure,
# where all CPUs (aka COREs) are inside a -single- NODE.
# At other locations, you may wish to consider some of the examples
# that follow below, after commenting out this ISU specific part.
if ($NCPUS > 1) then
switch (`hostname`)
case machinename:
# case se.msg.chem.iastate.edu:
# case sb.msg.chem.iastate.edu:
if ($NCPUS > 2) set NCPUS=4
set NNODES=1

This gives you parallel functionality, but it's still not using the machine resources (cores) correctly when I ask for anything more than 2 cores (always using only 2 cores).

[minor complaint]
Admittedly, I don't immediately get the logic of this section as currently coded, as one cannot get more than 2 cores to work in this case given how the if statements are written (so far as I can see now. I will assume I am the one missing something but have not decided to ask about it, instead changing the rungms text to the following). You can check this yourself by running top in another window. This is the most simple modification, and assumes you want to run N number of cores each time. Clearly, you can make this more elegant than it is (my modification, that is). Meantime, I want to run 4 cores on this machine, so I change the section to reflect a 4-core board (and commented out much of this section).
[/complaint]

# 2. This is an example of how to run on a multi-core SMP enclosure,
# where all CPUs (aka COREs) are inside a -single- NODE.
# At other locations, you may wish to consider some of the examples
# that follow below, after commenting out this ISU specific part.
if ($NCPUS > 1) then
switch (`hostname`)
case machinename
# case se.msg.chem.iastate.edu:
# case sb.msg.chem.iastate.edu:
# if ($NCPUS > 2) set NCPUS=2
# set NNODES=1
# set HOSTLIST=(`hostname`:cpus=$NCPUS)
# breaksw
# case machinename
# case br.msg.chem.iastate.edu:
if ($NCPUS >= 4) set NCPUS=4
set NNODES=1
set HOSTLIST=(`hostname`:cpus=$NCPUS)
breaksw
case machinename
# case cd.msg.chem.iastate.edu:
# case zn.msg.chem.iastate.edu:
# case ni.msg.chem.iastate.edu:
# case co.msg.chem.iastate.edu:
# case pb.msg.chem.iastate.edu:
# case bi.msg.chem.iastate.edu:
# case po.msg.chem.iastate.edu:
# case at.msg.chem.iastate.edu:
# case sc.msg.chem.iastate.edu:
# if ($NCPUS > 4) set NCPUS=4
# set NNODES=1
# set HOSTLIST=(`hostname`:cpus=$NCPUS)
# breaksw
# case ga.msg.chem.iastate.edu:
# case ge.msg.chem.iastate.edu:
# case gd.msg.chem.iastate.edu:
# if ($NCPUS > 6) set NCPUS=6
# set NNODES=1
# set HOSTLIST=(`hostname`:cpus=$NCPUS)
# breaksw
default:
echo I do not know how to run this node in parallel.
exit 20
endsw
endif
#

And, with this set of changes, I'm using all 4 cores on the board (but have some significant memory issues when running MP2 calks. But that's for another post).

The typical user will never be able to do what the GAMESS group has done in making an excellent program that also happens to be free. That said, the need to make changes to the rungms file is something that would be greatly simplified by having N number of rungms scripts for each case instead of a monolithic file that is mostly useless text to users not using one of the system types. This, for instance, would make rungms modification much easier. If I streamline rungms for my specific system, I may post a new file accordingly.