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Qsub Cannot Execute Binary File


As for why different operating systems (such as Windows, Mac OS X, and Linux) can't use the same binaries, consider this: What makes software objectively different to hardware? Sample: /home/home50/jsmith/a.out The following is a BAD way to do identify the location of your executable and will, most likely, cause you problems: ./a.out If you write your own programs, it As a monk, can I use Deflect Missiles to protect my ally? If you are not familiar with the terms MPI, OpenMPI, MPICH2, or LAM or if you don't know what the terms parallel or distributive mean, then: Your program is not parallel/distributive. http://amigasuperbit.com/cannot-execute/p4v-cannot-execute-binary-file.html

In you case the file was /home/golharr/workspace/BigDataScript/examples/test.bds.20150109_122430_716/task.line_7.id_2.exit Was the file created successfully and visible from the head node (where you are running bds)? In my environment, qsub rejects the command from stdin (I oversaw the pipe before). That could be the reason why you > stderr.cluster file was empty... > > — > Reply to this email directly or view it on GitHub > <#51 (comment)> > . more stack exchange communities company blog Stack Exchange Inbox Reputation and Badges sign up log in tour help Tour Start here for a quick overview of the site Help Center Detailed http://gridscheduler.sourceforge.net/howto/binarysubmit.html

Bash Cannot Execute Binary File Mac

Documentation For more information about the qsub command, see the man page (man qsub). 2010-8-27ACCC Systems Group Infolab wiki Search: Login Locked History Actions InfolabClusterCompute Menu Welcome to Since the submission script is nothing more than a regular shell script, the example should print out what host it is running on to our standard output file. #PBS -N my_job_name I am using Debian Squeeze Linux linux bash ssh debian share|improve this question edited Jun 12 '12 at 22:31 Oliver Salzburg♦ 56.7k37188245 asked Jun 12 '12 at 21:26 superuser 1,86131428 4 Additional delay Please note that requesting a specific node might cause an additional delay prior to your job execution as the resources on the specific node might not be available when

BigDataScript owner pcingola commented Jan 9, 2015 Can you execute the "bds exec" command from the slave node and check that it writes the file appropriately? (many clusters do not allow showq on the other hand displays all of the jobs. Interactive jobs on multiple nodes If you want to run your interactive job on multiple nodes you need to specify the number of nodes accordingly. Cannot Execute Binary File Centos If you would like to use 6 cores on a single node you could do it with the following directive: #PBS -l nodes=1:ppn=6Here is another example requesting two nodes with 32

Walltime MUST be requested using the format HHH:MM:SS and the system interprets the values from right to left. Bash Cannot Execute Binary File Linux golharam commented Jan 9, 2015 sure, ok. There should be 5 files there: task.line_7.id_2.stdout task.line_7.id_2.stderr task.line_7.id_2.exitCode task.line_7.id_2.stdout.cluster task.line_7.id_2.stderr.cluster The first three are the ones that bds-exec creates (and the oned bds needs to read). The wrapper script allows the submitter to use the standard submission flags, and it also accounts for the flags specified in the qtask file (which is used by qtcsh when transparently

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). Cannot Execute Binary File Cygwin The SGE parameter I use to force SGE to use bash in -S /bin/bash I think the best fix would be to have every parameter that you can pass to SGE If you provided the Name directive discussed in the previous section, then your default standard output will be saved to InfolabClusterTutorial.o711. I'll continue playing with it and keep you posted if any issues come up.

Bash Cannot Execute Binary File Linux

You can also use the qdel command that has the same effect as sending your job a SIGKILL signal: $ qsub outputjob.sh 60352.ilhead1.stanford.edu $ qdel 60352.ilhead1.stanford.eduIf you are using job arrays By default the resource manager will redirect all standard output of a job to a file named jobname.ojobid. Bash Cannot Execute Binary File Mac h is an abbreviation for huhohshdhjha a is an abbreviation for prsh [-t] show task information (implicitly -g t) [-u user_list] view only jobs of this user [-U user_list] select only Cannot Execute Binary File Java You are not limited to just what you see in the sample script.

For staff and faculty, the default is the staff queue. check my blog Or, it may never run because you requested too many resources or resources that will never be available to you. EOF
your job 47428 ("test") has been submitted Both techniques above take advantage of the fact that qsub uses the STDIN stream as a job script if you don't specify a script This is problematic as you would actually be passing the arguments to the qsub program instead of your own program. Cannot Execute Binary File Ubuntu

Then, no parameters are passed on the command line, everything is included in the shell script. But, after a minute or so, the job will cancel and a message like the following will be in your standard error file: -bash: line 1: /usr/spool/PBS/mom_priv/jobs/2256.argo-n.SC: cannot execute binary file As stated before, one core is the default. http://amigasuperbit.com/cannot-execute/python-cannot-execute-binary-file.html The default job launch mechanism is to echo the executable filename into the login shell's stdin?

What now? Docker Cannot Execute Binary File e.g. Or, include the cd command in your script.

The "cluster" files should mention that error, but "stderr.cluster" was empty...

As was explained, the name of the default is constructed from the following information: jobname.ejobid For example, if you submit the a.out job and the job is assigned the job number Now the has been fixed (version 0.999b). 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. Python Cannot Execute Binary File script_file must not be binary/executable file Never use qsub to submit a binary executable to the resource manager.

But something is still wrong. > My script has 1 line: > > task echo Hello world, task > > When I run the script using the command 'bds -s sge Related 36How can I resolve the error “cannot execute binary file”?0What can I do about “cannot execute binary file”0running sac2xy returns sac2xy: cannot execute binary file on osx 10.91./install_bam.sh and i You are STRONGLY encouraged to erase error files after reviewing the content. have a peek at these guys How can I fix this?

Another question: Is your cluster using NFS? Stdout len: 0 00:00:01.294 Error trying to find out post-mortem info on task (PID '11'). There should be 5 files there: task.line_7.id_2.stdout task.line_7.id_2.stderr task.line_7.id_2.exitCode task.line_7.id_2.stdout.cluster task.line_7.id_2.stderr.cluster The first three are the ones that bds-exec creates (and the ones bds needs to read). None of my environment settings are set in sh, only in my .bashrc.

It can be used as a "binary version" of qsub. Browse other questions tagged osx bash binary-files or ask your own question. 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 Now that I think about it, executing binaries should already work?

Typically the cause is running an executable on the wrong architecture - if you try to run x86 executables on an ARM CPU, this message comes up. When TORQUE attempts to run the job, it fails with the following > in the job stderr file: > > ------ > -bash: line 1: /usr/spool/PBS/mom_priv/jobs/10211.moab..SC: cannot > execute binary file 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 My regex has a double backslash and BDS is not matching my regex.

Lab colleague uses cracked software. If you submit a job that will run for an extended period of time (days or weeks), it's convenient to be informed of its completion.