Von: Mertens, Markus
Gesendet: Freitag, 18. Januar 2019 11:22
An: firma@tange.dk
Betreff: GNU parallel: bug found message
Gesendet: Freitag, 18. Januar 2019 11:22
An: firma@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
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
Dr. Maren Thäter (Vorsitz)
Dr. Matthias Ernst
Vorsitzender des Aufsichtsrates
Dr. Rainer Norden