Hi, sorry to ressurect this yet again. I'm still getting problems unfortunately and would appreciate your help please. I've found a work around but its messy and brittle and I have to be doing something wrong here to be causing it.
The .webmo_profile environmental control doesn't seem to be working as I expect it. This is what it is set to currently:
Code: Select all
$ cat /usr/local/webmo/private/webmo/.webmo_profile
source /home/support/apps/intel/15.0.6/composer_xe_2015.6.233/bin/compilervars.sh intel64
source /etc/profile.d/modules.sh
module use /home/support/modulefiles
module load intel/15.0.6/composer_xe_2015.6.233 apps gaussian/intel/15.0.6/g09
That should set the environment up to run gaussian properly, including populating the LD_LIBRARY_PATH variable. Submitting to the queue
Code: Select all
sbatch -J WebMO_2 --reservation=webmo -o /usr/local/webmo/private/webmo/graeme/2/pbs_stdout -e /usr/local/webmo/private/webmo/graeme/2/pbs_stderr -p 'compute' --nodes=1 --tasks-per-node=16 /usr/local/webmo/private/webmo/graeme/2/pbs_script.sh
Leads to Gaussian jobs would failing with:
Code: Select all
[webmo@hprc-guest-114-253 gaussian_job]$ cat /usr/local/webmo/private/webmo/graeme/2/output.log
/home/support/apps/apps/gaussian/intel/15.0.6/g09/g09: error while loading shared libraries: libmkl_intel_ilp64.so: cannot open shared object file: No such file or directory
The LD_LIBRARY_PATH the run_gaussian.cgi script seemed to be picking up was:
Code: Select all
/home/support/apps/apps/gaussian/intel/15.0.6/g09/bsd:/home/support/apps/apps/gaussian/intel/15.0.6/g09/local:/home/support/apps/apps/gaussian/intel/15.0.6/g09/extras:/home/support/apps/apps/gaussian/intel/15.0.6/g09
Which did not include the necessary path to where libmkl_intel_ilp64.so is.
To get gaussian jobs to run it was necessary to explicitly set the LD_LIBRARY_PATH in /usr/local/webmo/public_html/cgi-bin/webmo/run_gaussian.cgi
Code: Select all
$ diff -u /usr/local/webmo/public_html/cgi-bin/webmo/run_gaussian-backup.cgi /usr/local/webmo/public_html/cgi-bin/webmo/run_gaussian.cgi
--- /usr/local/webmo/public_html/cgi-bin/webmo/run_gaussian-backup.cgi 2020-07-22 13:35:57.770487800 +0100
+++ /usr/local/webmo/public_html/cgi-bin/webmo/run_gaussian.cgi 2020-07-22 15:11:04.992462468 +0100
@@ -62,7 +62,9 @@
$ENV{'GAUSS_ARCHDIR'} = $GAUSS_ARCHDIR;
$ENV{'GMAIN'} = $GMAIN;
$ENV{'PATH'} = $ENV{'PATH'}.":".$ENV{'GAUSS_EXEDIR'};
-$ENV{'LD_LIBRARY_PATH'} = $LD_LIBRARY_PATH;
+#$ENV{'LD_LIBRARY_PATH'} = $LD_LIBRARY_PATH;
+$ENV{'LD_LIBRARY_PATH'} = '/home/support/apps/intel/15.0.6/composer_xe_2015.6.233/compiler/lib/intel64:/home/support/apps/intel/15.0.6/composer_xe_2015.6.233/mpirt/lib
/intel64:/home/support/apps/intel/15.0.6/composer_xe_2015.6.233/ipp/lib/intel64:/home/support/apps/intel/15.0.6/composer_xe_2015.6.233/ipp/tools/intel64/perfsys:/home/s
upport/apps/intel/15.0.6/composer_xe_2015.6.233/mkl/lib/intel64:/home/support/apps/intel/15.0.6/composer_xe_2015.6.233/tbb/lib/intel64/gcc4.4:/home/support/apps/intel/1
5.0.6/composer_xe_2015.6.233/debugger/libipt/intel64/lib:/home/support/apps/apps/gaussian/intel/15.0.6/g09/bsd:/home/support/apps/apps/gaussian/intel/15.0.6/g09/local:/
home/support/apps/apps/gaussian/intel/15.0.6/g09/extras:/home/support/apps/apps/gaussian/intel/15.0.6/g09';
+print "LD_LIBRARY_PATH = $LD_LIBRARY_PATH\n";
# if we are using PBS, find out which host we are running on
if ($externalBatchQueue)
Which is a bit of a cludge.
What have I missed here? I have to be doing something wrong.
Thanks in advance.
Sean