TURBOMOLE Users Forum
Installation and usage of TURBOMOLE => Parallel Runs => Topic started by: jbaltrus on March 04, 2014, 11:43:13 PM
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Dear all,
I am trying to run TURBOMOLE on my newly installed cluster with SGE on it. I do everything as I should, e.g. add following lines to bash.profile
export TURBODIR=/home/jbaltrus/turbolinux_65/TURBOMOLE
export PATH=$TURBODIR/scripts:$PATH
export PATH=$TURBODIR/bin/em64t-unknown-linux-gnu_mpi:$PATH
ulimit -s unlimited
PATH=$PATH:$HOME/bin
export PATH
but still optimization aborts right away with bunch of lines which I can;'t interpret, it seems like it starts OK but where it fails is unclear. Perhaps anyone has ideas?
thanks
Jonas
\\Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
/home/jbaltrus/turbolinux_65/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/sdg: line 1: ../em64t-unknown-linux-gnu/sdg: No such file or directory
ridft program used is /home/jbaltrus/turbolinux_65/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/ridft
rdgrad program used is /home/jbaltrus/turbolinux_65/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/rdgrad
relax program used is /home/jbaltrus/turbolinux_65/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/relax
frog program used is /home/jbaltrus/turbolinux_65/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/frog
uff program used is /home/jbaltrus/turbolinux_65/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/uff
convgrep will be taken out of the TURBODIR directory
define program used is /home/jbaltrus/turbolinux_65/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/define
statpt program used is /home/jbaltrus/turbolinux_65/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/statpt
aoforce program used is /home/jbaltrus/turbolinux_65/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/aoforce
/home/jbaltrus/turbolinux_65/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/ridft: line 1: ../../mpirun_scripts/ridft: No such file or directory
ERROR in dscf step
Please look at the output file job.last
Possible reasons:
- unfinished step before running energy calculation
-> call \'actual -r\' and restart job
- missing input files like coord, basis, control, ...
-> rerun define
- missing auxiliary basis set if using RI
-> switch on RI in define
- mismatch between occupation and provided MOs
-> rerun define and redo \'eht\' step
/home/jbaltrus/turbolinux_65/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/aoforce: line 1: ../em64t-unknown-linux-gnu/aoforce: No such file or directory
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Hi Jonas,
It's best to use the 'sysname' script to set the PATH to Turbomole executables:
http://www.cosmologic.de/data/DOK_HTML/node13.html
For example:
export PATH=$PATH:$TURBODIR/scripts
export PATH=$TURBODIR/bin/`sysname`:$PATH
In particular, it's best to avoid appending '_mpi', '_smp' or any other qualifiers manually. If you want to run MPI jobs, just set
export PARA_ARCH=MPI
and redo
export PATH=$TURBODIR/bin/`sysname`:$PATH
(here it's important to put the "new" path before $PATH)
in your job script. Getting all the parallel schemes to work smoothly can take some time (http://www.cosmologic.de/data/DOK_HTML/node25.html), but generally things should work fine as long as you make sure that your PATH is updated in your SGE job script. The sample PBS script in the manual also outlines nicely the main points (http://www.cosmologic.de/data/DOK_HTML/node39.html). Exporting the whole environment with -V is also important (the same switch should work for SGE).
Best,
Antti
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Hello Jonas,
/home/jbaltrus/turbolinux_65/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/sdg: line 1: ../em64t-unknown-linux-gnu/sdg: No such file or directory
the sdg program is just a symbolic link to the serial version:
lrwxrwxrwx 1 huniar users 30 2013-03-05 17:12 sdg -> ../em64t-unknown-linux-gnu/sdg
the error you get could stem from the fact that there are no serial binaries installed in /home/jbaltrus/turbolinux_65/TURBOMOLE/bin/em64t-unknown-linux-gnu/ - could that be? Or is there a problem with file permissions (e.g. if you unpack the official Turbomole as root or with sudo)?
Regards,
Uwe