Compiling And Running GAMESS-US (1 May 2013(R1)) On 64-bit Ubuntu 12.X/13.X In SMP Mode
April 5th, 2014
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 -dumpversionGNU 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.targamess/ 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 ./configThis 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:
linux64Where 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):
gfortrangfortran 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:
4.4Alas, your version of gfortran does not support REAL*16, so relativistic integrals cannot use quadruple precision. Other than this, everything will work properly. hitto 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':
atlasWhere 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/atlasThe 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 hitto 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 hitto 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.
sockets64 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):
noYour 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 -pnet.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.
