Hello Michael, I don't know if this one has been answered already. It has puzzled me for some time and I couldn't find a reply to your message. Anyway here is my recipe that works with CCP4 6.0.2, CCP4i 1.4.4.2 and OpenPBS/Torque 2.1.6 on Fedora Core 5. If you have a look in the file .../ccp4i/src/local.tcl, "generic" batch jobs are started with "$batch_queue $batch_options source $com_file"; OpenPBS doesn't neeed the inserted "source". A special case has been defined for the SGE batch type which will work for PBS. So if you don't want to modify the tcl source, a workaround would be to open CCP4i>System Administration>Configure Interface and define the batch queue as a Sun Grid Engine. Fill the batch command at least with a qsub -V for OpenPBS to keep the environment variables (maybe a -cwd if your qsub version implements it). On top of the interface, fill the "Command to set up CCP4 (used by remote jobs)" with cd $PBS_O_WORKDIR otherwise your home directory will be trashed with data files. Check that TEMPORARY and CCP4_SCR are the same. Regards, Alain Michael Weyand wrote: > Dear colleagues, > > I have problems to start jobs from the CCP4i by using the (OpenPBS) > batch queing system on our Linux cluster > Here are some machine details > > System software > Suse Linux 9.3, 2.6.11.4-20a-smp Kernel > Batch-Queing-System: OpenPBS > > CCP4 version 6.0, binary download; everything works fine by direct job > submitting > > First I tried to start the jobs by configuring the interface, > adressing a PBS system and some qsub options in the command line, like > 'qsub -q small -N ccp4-weyand' . But I always got the following pop-up > message, independent of the used options or without any qsub options: > > qsub-error-message > <ftp://ftp.mpi-dortmund.mpg.de/pub/weyand/qsub_error.png> > > My interpretation is that the qsub command is executed, but maybe with > the wrong options?? > > > Then I did some reading (always good!!) and found some hints on the > CCP4 homepage doing some scripting for a Condor system. > > I wrote a script for our PBS queues. May be not clever, but it worked. > At least partly: I was able to start jobs via CCP4i, and I got the > right output files in the right folders, but the relevant CCP4i > project 'database.def' file was not updated. The job list was extended > by the new job, but no entries for the output files were added. So, > this option is also useless. > Here is my script, which I started within a CCP4i queue command line, > like '/home/weyand/myqsub' > > ----> SNIP > #!/bin/sh > > rm -f ccp4ish.sh > rm -f ccp4.pbs > > ####create ccp4ish.sh > > sh1="#!/bin/csh -f" > sh2=${1+"$@"} > > echo $sh1 > ccp4ish.sh > echo $sh2 >> ccp4ish.sh > > chmod 755 ccp4ish.sh > exe="./ccp4ish.sh" > > echo "#PBS -l nodes=1:ppn=1" > ccp4.pbs > echo "#PBS -N ccp4_$USER" >> ccp4.pbs > echo "#PBS -q small" >> ccp4.pbs > echo "cd `pwd`" >> ccp4.pbs > > echo $exe >> ccp4.pbs > > ### submit to PBS > qsub ccp4.pbs > > echo "echo "Job finished on: " `date`" >> ccp4.pbs > > echo "exit 0" >> ccp4.pbs > -----> SNIP > > Summary > I address here maybe two problems: > 1. why is the internal PBS/qsub option is not working on our system? > 2. why is my script (which leads to an executed (!) CCP4i job) not > updating the database file properly? > > If there is someone who can at least give hints for solving one > problem, I would forget the second... > > Any comments are highly appreciated. > > Regards > Michael