mpi-selector --set intel_mpi-5.0.1.035
qsub -I -l select=ncpus=1:mem=2g -l walltime=5:0:0
source /opt/intel/composerxe/bin/compilervars.sh intel64
ifort -v
ifort version 15.0.2
tar -xzf gamess-current.tar.gz -C ~/
cd ~/gamess
cd ~/gamess ./config
Ниже приведено выводимое скриптом и что нужно вводить в ответ (жирным). В некоторых случаях нужно просто нажимать клавишу 'Enter':
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 <return>. 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 <return> to go on.
Нажать '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 (Q model), these are 64 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:
Ввести linux64, нажать Enter
Where is the GAMESS software on your system? A typical response might be /u1/mike/gamess, most probably the correct answer is /mnt/storage/home/login/gamess GAMESS directory? [/mnt/storage/home/login/gamess]
Нажать Enter
Setting up GAMESS compile and link for GMS_TARGET=linux64 GAMESS software is located at GMS_PATH=/mnt/storage/home/login/gamess Please provide the name of the build locaation. This may be the same location as the GAMESS directory. GAMESS build directory? [/mnt/storage/home/login/gamess]
Нажать 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]
Нажать Enter
Linux offers many choices for FORTRAN compilers, including the GNU compiler suite's free compiler 'gfortran', usually included in any Linux distribution. If gfortran is not installed, it can be installed from your distribution media. To check on installed GNU compilers, for RedHat/SUSE style Linux, type 'rpm -aq | grep gcc' for both languages, and for Debian/Ubuntu style Linux, it takes two commands type 'dpkg -l | grep gcc' type 'dpkg -l | grep gfortran' There are also commercial compilers, namely Intel's 'ifort', and Portland Group's 'pgfortran', and Pathscale's 'pathf90'. The last two are not common, and aren't as well tested. type 'which gfortran' to look for GNU's gfortran (a good choice), type 'which ifort' to look for Intel's compiler (a good choice), 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:
ifort
Use of 'ifort' requires additional information since library
names, and compiler flags, are very version number specific.
note: ifort's directory tree is typically
/opt/intel/fc
/opt/intel/fce
/opt/intel/Compiler
/opt/intel/composerxe (et cetera).
Type 'which ifort' and note the version number in its pathname.
In case of the newer 'composerxe' bundles, the version is not
shown in the pathname, but can be obtained by 'ifort -V'.
Enter only the main version number, such as 8, ... 11, 12, 13, 14.
Version?
15
hit <return> to continue to the math library setup.
Нажать 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':
mkl
The exact MKL libraries needed depend on its version number.
First, where is your MKL software installed? For example
/opt/intel/mkl -or-
/opt/intel/Compiler/mkl -or-
/opt/intel/composerxe/mkl -or-
/shared/intel/composer_xe_2013/mkl -or-
/your/sites/nonstandard/path/mkl
Don't enter anything past the mkl subdirectory pathname.
MKL pathname?
/opt/intel/composerxe/mkl
Second, it is possible to have multiple version of MKL installed, but often there is only one version installed. Your system seems to have the following version(s): benchmarks bin examples include interfaces lib tests tools a) If the above output contains one or more version number, enter the specific version you prefer, giving all decimals. b) If the above output contains paths like 'bin' and 'lib', enter the word 'skip' next. MKL version (or 'skip')?
skip
Math library 'mkl' will be taken from /opt/intel/composerxe/mkl/lib/intel64 please hit <return> to compile the GAMESS source code activator
Нажать Enter
ifort -o /mnt/storage/home/login/gamess/tools/actvte.x actvte.f unset echo Source code activator was successfully compiled. please hit <return> to set up your network for Linux clusters.
Нажать 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')?
mpi
The MPI libraries which work well on linux64/Infiniband are
Intel's MPI (impi)
MVAPICH2
SGI's mpt from ProPack, on Altix/ICE systems
Other libraries may work, please see 'readme.ddi' for info.
The choices listed above will compile and link easily,
and are known to run correctly and efficiently.
Enter 'sockets' if you just changed your mind about trying MPI.
Enter MPI library (impi, mvapich2, mpt, sockets):
impi
MPI can be installed in many places, so let's find impi.
The person who installed your MPI can tell you where it really is.
impi is probably located at a directory like
/opt/intel/impi/3.2
/share/apps/intel/impi/4.0.1.007
/share/apps/intel/impi/4.0.2.003
/shared/intel/impi/4.1.0.024
include iMPI's version numbers in your reply.
Please enter your impi's location:
/opt/intel/impi/5.0.1.035
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
/mnt/storage/home/login/gamess/install.info
Now, please follow the directions in
/mnt/storage/home/login/gamess/machines/readme.unix
set MAXCPUS=32 set MAXNODES=1024
cd ~/gamess/ddi ./compddi
cd ~/gamess ./compall
======================== mpchbond ============================== Mon Feb 8 18:40:06 NOVT 2016 Copying source code, mpchbond.src does not require activation. ifort -c -i8 -O2 -ftz -auto -assume byterecl -vec-report0 -warn nousage -inline-level=0 mpchbond.f90 ifort: command line remark #10010: option '-vec-report0' is deprecated and will be removed in a future release. See '-help deprecated' unset echo Mon Feb 8 18:40:07 NOVT 2016 0.684u 0.044s 0:00.86 83.7% 0+0k 8+1120io 0pf+0w
cd ~/gamess ./lked gamess 00
set TARGET=sockets set GMSPATH=/u1/mike/gamess
на
set TARGET=mpi set GMSPATH=~/gamess
if ($TARGET == XXX) then ... endif
для всех XXX, кроме 'mpi'.
if ($TARGET == mpi) then ... endif
set PPN=$4
set DDI_MPI_CHOICE=impi
if ($DDI_MPI_CHOICE == impi) then
set DDI_MPI_ROOT=/opt/intel/impi/5.0.1.035/intel64
endif
# setenv I_MPI_FABRICS dapl
# setenv LD_LIBRARY_PATH /shared/intel/composer_xe_2013.1.117/compiler/lib/intel64:$LD_LIBRARY_PATH
set SCR=~/tmp set USERSCR=~/gamess.results
if ($SCHED == PBS) then # our ISU clusters have different names for local working disk space. # if ($?TMPDIR) then # set SCR=$TMPDIR # else # set SCR=/scratch/$PBS_JOBID # endif echo "PBS has assigned the following compute nodes to this run:" uniq $PBS_NODEFILE endif
./rungms exam$NUM $VERNO 1 >& exam$NUM.log
в
./rungms exam$NUM $VERNO 1 1 >& exam$NUM.log
т.к. при использовании MPI 'rungms' должен получать 4 параметра.
rm exam??.log
cd ~/gamess ./runall 00
tests/standard/checktst
Должно быть выведено примерно такое:
Checking the results of your sample GAMESS calculations, the output files (exam??.log) will be taken from . All jobs terminated normally, now checking detailed numerical results exam01: Eerr=0.0e+00 Gerr=0.0e+00. Passed. ... exam46: B1err=0.0e+00 A1err=0.0e+00. Passed. exam47: Serr=0.0e+00 Perr=5.0e-10. Passed. All 47 test results are correct!