________________________________ Von: Mertens, Markus Gesendet: Freitag, 18. Januar 2019 11:22 An: fi...@tange.dk Betreff: GNU parallel: bug found message
Dear Dr. Tange, after reading your book "GNU parallel 2018" I still have no idea how to start GNU parallel with systemd as backgroud service under linux. The following script does not work because parallel assumes somehow that it should create a directory. But this already exists and I have all permissions for it. Parallel itself believes that I have found a bug: [...]$ bash /projects/freesurfer/bin/run_parallel_freesurfer.sh 10 :,thalamus_nfs Academic tradition requires you to cite works you base your article on. When using programs that use GNU Parallel to process data for publication please cite: O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47. This helps funding further development; AND IT WON'T COST YOU A CENT. If you pay 10000 EUR you should feel free to use GNU Parallel without citing. To silence this citation notice: run 'parallel --citation'. parallel: This should not happen. You have found a bug. Please contact <parallel@gnu.org> and include: * The version number: 20170322 * The bugid: host check too many col0: thalamus_nfs mkdir: cannot create directory '/projects/freesurfer': Permission denied * The command line being run * The files being read (put the files on a webserver if they are big) If you get the error on smaller/fewer files, please include those instead. [...]$ [...]$ [...]$ cat run_parallel_freesurfer.sh #!/bin/bash jobs=$1 hosts=$2 ( exec tail -f -n +1 $FREESURFER_PATH/config/_joblist_ & echo $! >$FREESURFER_PATH/config/tail.pid ) | parallel --workdir $SUBJECTS_DIR -u -j$jobs --filter-hosts -S $hosts -u [...]$ [...]$ [...]$ echo $FREESURFER_PATH $SUBJECTS_DIR /projects/freesurfer /projects/freesurfer/subjects [...]$ Once the script is working I would like to run it via systemd like "nohup bash /projects/freesurfer/bin/run_parallel_freesurfer.sh 10 :,thalamus_nfs &". Will this be possible? Kind regards, Markus Mertens _______________________________________________________________ Evangelisches Klinikum Bethel gGmbH Akademisches Lehrkrankenhaus der Universität Münster Sitz der Gesellschaft Kantensiek 11 | 33617 Bielefeld Amtsgericht Bielefeld HRB 30169 Geschäftsführer Dr. Maren Thäter (Vorsitz) Dr. Matthias Ernst Vorsitzender des Aufsichtsrates Dr. Rainer Norden
