Do not hardcode ***homedir*** into the script: WRONG: ***homedir***/a.out.error Replace the ***homedir*** with the path to your home directory. asked 4 years ago viewed 296759 times active 1 year ago Visit Chat Linked 0 Shell Script “cannot execute binary file” Related 0Bin file installation problem: “cannot execute binary file”2How do Where are my jobs This is particularly useful if you want to run an interactive session over more than one node (as you will only get a single command prompt). You have probably already noticed the first workaround in the text above. check over here
I was told that some slow > NFS systems take a few seconds to update file status...(as opposed to > infiniband or other options). > > — > Reply to this Example, first using empty 'clusterRunAdditionalArgs' runs the same as before (output edited for readability): $ bds -s cluster -d z.bds ... 00:00:00.269 Adding clusterRunAdditionalArgs. This might be caused because the regular expression (see bds.config pidRegex entry) is not catching you cluster's task ID returned by qsub. We recommend upgrading to the latest Safari, Google Chrome, or Firefox. http://gridscheduler.sourceforge.net/howto/binarysubmit.html
Use 3 nodes but only one core per node: qsub -V -l nodes=3:ppn=1 -q staff my_script Use 3 nodes and two core per node: qsub -V -l nodes=3:ppn=2 -q staff my_script SGE.parameters works (I think) … On Fri, Jan 9, 2015 at 4:04 PM, Pablo Cingolani ***@***.***> wrote: Yes, I'm working on that. You are not required to use the C-shell.
The downside - each new submission creates a new error file, cluttering your home directory with hundreds of them. If you don't include the line and it's not required, then the default scheme is used. I change my bds.config to have: pidRegex = "Your job (\d+)" Then, test_01.bds: #!/usr/bin/env bds task echo Hello world My SGE cluster has a parallel environment called pe (not orte). Cannot Execute Binary File Centos The following request for a single node is unnecessary: qsub -V -l nodes=1 -q staff my_script It's the same as doing: qsub -V -q staff my_script If you will be running
Is it necessary to pipe the command into qsub? Bash Cannot Execute Binary File Linux So... Why did Borden do that to his wife in The Prestige? check it out Another question: Is your cluster using NFS?
Then, on a line by itself, type the
? Cannot Execute Binary File Cygwin Please consult the cluster's hardware capabilities before using this directive. The resources (not just cores but other requested resources including but not limited to nodes) may be owned by another job and, when that job completes and the resource(s) become available, As a monk, can I use Deflect Missiles to protect my ally?
Instead, your job does not run because the system will be unable to satisfy your request. http://accc.uic.edu/answer/how-do-i-run-programs-argo I am trying to execute the file on OSX using $ ./b1 I get the following error: -bash: ./b1: cannot execute binary file I've looked at other similar questions, but to Bash Cannot Execute Binary File Mac Is there a chance that your cluster is configured to merge STDERR and STDOUT when using "-o" command line option in "qsub"? Cannot Execute Binary File Java Then, no parameters are passed on the command line, everything is included in the shell script.
In my bds.config I have: taskShell = /bin/bash -e … On Fri, Jan 9, 2015 at 3:11 PM, Pablo Cingolani ***@***.***> wrote: Added 'taskShell' and 'sysShell' as options to bds.config file: check my blog Commands such as halt, poweroff, reboot will return command not found. Here is an example of an interactive run: ~$ hostname ilhead1.Stanford.EDU ~$ qsub -I -l nodes=1:ppn=32 qsub: waiting for job 44389.ilhead1.stanford.edu to start qsub: job 44389.ilhead1.stanford.edu ready ~$ hostname iln27.stanford.edu ... Users should direct a job to a queue and not to nodes: Wrong: qsub -V -l nodes=argo1-1 my_script Right: qsub -V -1 nodes=1 -q student_long my_script Wrong: qsub -V -l nodes=argo1-1+argo1-2 Cannot Execute Binary File Ubuntu
Use your CS credentials to log in. Do you think some of the features in your package (currently missing from bds) could be added? I know this because: The file b1 is in the ELF (Extensible and Linkable Format) format, while Mac OS X uses the Mach-O format for binaries; file recognizes this file is this content How can I fix this?
The downside - each new submission creates a new error file, cluttering your home directory with hundreds of them. Docker Cannot Execute Binary File Both require an agreed language to get work done. I see in your code that you look for some particular column ??
The last two files are create by the cluster system (bds ignores them). — Reply to this email directly or view it on GitHub <#51 (comment)> . What is mounted under /dfs /dfs/scratch0 points to a big scratch volume on il-nfs-1 /dfs/scratch1 points to a big scratch volume on il-nfs-1 /dfs/ilfs2/0 points to the ilfs2 file server Passing To change the email destination, modify the content of the .forward file in your home directory. Python Cannot Execute Binary File This may be useful in a situation where you know your job should run no longer than 2 hours and if it runs longer then something went wrong.
If this is in fact the cause of the problem, then at least you will have narrowed it down. ...regards...dac ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu Thanks everyone for your inputs! –superuser Jun 13 '12 at 4:18 add a comment| up vote 9 down vote Try to run it using ./executablefilename instead of using sh executablefilename. I didn't see anything in what you reported that looks > wrong, so you will probably have to poke around yourself. have a peek at these guys BigDataScript owner pcingola commented Jan 8, 2015 @golharam I've added a new command line option '-checkPidRegex', here is how to use it: $ echo "Your job 18157" | bds -checkPidRegex Matching
You should also make sure to always use a full (absolute) path specification. Examples: Put the walltime on the qsub line: qsub -V -l nodes=1 -l walltime=720:00:00 -q staff my_script Put the walltime in the script file: #PBS -l walltime=720:00:00 and submit the script BigDataScript owner pcingola commented Jan 11, 2015 @golharam It would be interesting to take a look at it. unless the cluster crashes...
golharam commented Jan 9, 2015 I think it might be better for BDS to put all the commands it wants to run in a shell script that follows a user-defined or The following will send you and e-mail both when the job starts executing and when it finishes. #PBS -m be -M [email protected] sure that you supply a valid @stanford.edu or @cs.stanford.edu The right way of submitting a lot of jobs is to use job arrays. Now the has been >> fixed (version 0.999b).
e.g. golharam commented Jan 6, 2015 I see this same problem. I warned you not to shut the system down :P Can you get console access to it (physical monitor+keyboard attached)? How to delete the lines from a file that do not contain dot?
Can Trump undo the UN climate change agreement? Issue #51">Addded 'pidColumnCheckTaskRunning' in config file. The last two files are created by the cluster system (bds ignores them). Now that I think about it, executing binaries should already work?
However, if you request resources that will never be available ("I want eight cores on one node" is an example of a nonexistent resource), your job will never run. The 1st one is more likely as I would expect the second problem to give the error "Path not found". Don't worry, we'll talk more about those later.