[Iplant-api-dev] Odd Failures of Public Apps
Duvick, Jonathan P [GDCBS]
jduvick at iastate.edu
Tue May 19 15:09:41 MST 2015
I have had a similar error (including zero output) with the public app, 'gth-stampede-1.6.5u2'. This was the case for a job I just ran minutes ago (i.e. the problem is still out there).
"}Lmod Warning: /opt/modulefiles/TACC-paths: (TACC-paths): couldn't read file
"/opt/modulefiles/TACC-paths": no such file or directory "
Interestingly, I did NOT have a problem with a different public app, 'rb-Geneseqer-tiny-5.0.0', which ran earlier today, but I have 4 reps of failure with the above-mentioned 'gth-stampede-1.6.5u2'
Jon
Jon Duvick
PlantGDB Manager
http://www.plantgdb.org/
Department of Genetics, Development and Cell Biology
2258 Molecular Biology Building
Iowa State University
Ames IA 50011
(515) 294-2360
(515) 294-6755 FAX
________________________________
From: iplant-api-dev-bounces at iplantcollaborative.org <iplant-api-dev-bounces at iplantcollaborative.org> on behalf of Rion Dooley <dooley at tacc.utexas.edu>
Sent: Tuesday, May 19, 2015 4:08 PM
To: Duvick, Jonathan P [GDCBS]
Cc: iPlant API Developers Mailing List
Subject: Re: [Iplant-api-dev] Odd Failures of Public Apps
TACC had some file system issues over the last week and the DS was being sketchy about generating checksums, which is what Agave uses to verify public apps have not been corrupted. I’d put my money on the issues lying there before looking anywhere else.
—
Rion
On May 19, 2015, at 4:04 PM, Barthelson, Roger A - (rogerab) <rogerab at email.arizona.edu<mailto:rogerab at email.arizona.edu>> wrote:
I’ve had 3 different public apps fail repeatedly in the past week with error messages in the .err files. The jobs may not fail officially, but the outputs are 0 bytes. Below are the .err file contents. Any ideas? These were all functioning apps, tested successfully in the public form. They have something like this in the .err output: "Lmod Warning: /opt/modulefiles/TACC-paths: (TACC-paths): couldn't read file
"/opt/modulefiles/TACC-paths": no such file or directory"
Roger
BAYESEMBLER
{
"status" : "success",
"message" : null,
"version" : "2.1.0-r6d11c",
"result" : { }
}Lmod Warning: /opt/modulefiles/TACC-paths: (TACC-paths): couldn't read file
"/opt/modulefiles/TACC-paths": no such file or directory
While processing the following module(s):
Module fullname Module Filename
--------------- ---------------
TACC-paths /opt/modulefiles/TACC-paths
TACC /opt/modulefiles/TACC
Lmod Warning: /opt/modulefiles/cluster-paths: (cluster-paths): couldn't read
file "/opt/modulefiles/cluster-paths": no such file or directory
While processing the following module(s):
Module fullname Module Filename
--------------- ---------------
cluster-paths /opt/modulefiles/cluster-paths
[bam_cat] ERROR: fail to open file 'TrmPr1_SRR567164.sra_1.fastq.bam' 'TrmPr1_SRR567165.sra_1.fastq.bam'.
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
[bam_sort_core] truncated file. Continue anyway.
[bam_cat] ERROR: fail to open file 'TrmPr1_SRR567164.sra_1.fastq.bam' 'TrmPr1_SRR567165.sra_1.fastq.bam'.
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
[bam_sort_core] truncated file. Continue anyway.
[bam_sort_core] merging from 2 files...
/tmp/slurmd/job5233479/slurm_script: line 92: ./bayesembler: Text file busy
real 0m0.066s
user 0m0.001s
sys 0m0.001s
{
"status" : "success",
"message" : null,
"version" : "2.1.0-r6d11c",
"result" : { }
}/tmp/slurmd/job5233480/slurm_script: line 92: ./bayesembler: Text file busy
real 0m0.005s
user 0m0.000s
sys 0m0.001s
{
"status" : "error",
"message" : "Job 0001431121365252-5056a550b8-0001-007 is not running.",
"version" : "2.1.0-r6d11c"
}
GMAP
{
"status" : "success",
"message" : null,
"version" : "2.1.0-r6d11c",
"result" : { }
}Lmod Warning: /opt/modulefiles/TACC-paths: (TACC-paths): couldn't read file
"/opt/modulefiles/TACC-paths": no such file or directory
While processing the following module(s):
Module fullname Module Filename
--------------- ---------------
TACC-paths /opt/modulefiles/TACC-paths
TACC /opt/modulefiles/TACC
Lmod Warning: /opt/modulefiles/cluster-paths: (cluster-paths): couldn't read
file "/opt/modulefiles/cluster-paths": no such file or directory
While processing the following module(s):
Module fullname Module Filename
--------------- ---------------
cluster-paths /opt/modulefiles/cluster-paths
-k flag not specified, so building with default 15-mers and base size 12-mers
Sorting chromosomes in chrom order. To turn off or sort other ways, use the -s flag.
Running .//fa_coords -o ./genome.coords -k 14 BAgenomeRay41.fa
Unknown option: k
Can't open file 14 at .//fa_coords line 156.
.//fa_coords -o ./genome.coords -k 14 BAgenomeRay41.fa failed with return code 512 at ./gmap_build line 135.
GMAP version 2013-09-11 called with args: gmap -D genome -d genome -t 8 -n 14 -f 4 BAsoaptrans25sl200.fa
Checking compiler assumptions for popcnt: 6B8B4567 clz=1 clz=0 popcount=17
Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1
Checking compiler assumptions for SSE4.1: 103 -58 max=103
Unable to find genome directory genome. Either recompile the GMAP package
to have the correct default directory (seen by doing gmap --version),
or use the -D flag to gmap to specify the correct genome directory.
tar: genome: Cannot stat: No such file or directory
tar: Exiting with failure status due to previous errors
rm: cannot remove `genome': No such file or directory
{
"status" : "success",
"message" : null,
"version" : "2.1.0-r6d11c",
"result" : { }
}
GENESEQER-MIDSIZE
{
"status" : "success",
"message" : null,
"version" : "2.1.0-r6d11c",
"result" : { }
}Lmod Warning: /opt/modulefiles/TACC-paths: (TACC-paths): couldn't read file
"/opt/modulefiles/TACC-paths": no such file or directory
While processing the following module(s):
Module fullname Module Filename
--------------- ---------------
TACC-paths /opt/modulefiles/TACC-paths
TACC /opt/modulefiles/TACC
Lmod Warning: /opt/modulefiles/cluster-paths: (cluster-paths): couldn't read
file "/opt/modulefiles/cluster-paths": no such file or directory
While processing the following module(s):
Module fullname Module Filename
--------------- ---------------
cluster-paths /opt/modulefiles/cluster-paths
/tmp/slurmd/job5264270/slurm_script: line 95: ../MakeArray: Text file busy
/tmp/slurmd/job5264270/slurm_script: line 95: ../MakeArray: Text file busy
/tmp/slurmd/job5264270/slurm_script: line 95: ../MakeArray: Text file busy
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][spawn_processes] Failed to execvp() '/scratch/0004/iplant/rogerab/job-0001431539033040-5056a550b8-0001-007-60eb1ec2-3ace-4d2a-b376-7194958dc7ca_0001/GeneSeqerMPI': ��� (26)
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][spawn_processes] Failed to execvp() '/scratch/0004/iplant/rogerab/job-0001431539033040-5056a550b8-0001-007-60eb1ec2-3ace-4d2a-b376-7194958dc7ca_0001/GeneSeqerMPI': �%� (26)
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI process (rank: 0, pid: 90468) exited with status 1
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][spawn_processes] Failed to execvp() '/scratch/0004/iplant/rogerab/job-0001431539033040-5056a550b8-0001-007-60eb1ec2-3ace-4d2a-b376-7194958dc7ca_0001/GeneSeqerMPI': ��� (26)
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI process (rank: 4, pid: 90480) exited with status 1
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][spawn_processes] Failed to execvp() '/scratch/0004/iplant/rogerab/job-0001431539033040-5056a550b8-0001-007-60eb1ec2-3ace-4d2a-b376-7194958dc7ca_0001/GeneSeqerMPI': ��� (26)
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][spawn_processes] Failed to execvp() '/scratch/0004/iplant/rogerab/job-0001431539033040-5056a550b8-0001-007-60eb1ec2-3ace-4d2a-b376-7194958dc7ca_0001/GeneSeqerMPI': ��� (26)
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][spawn_processes] Failed to execvp() '/scratch/0004/iplant/rogerab/job-0001431539033040-5056a550b8-0001-007-60eb1ec2-3ace-4d2a-b376-7194958dc7ca_0001/GeneSeqerMPI': ��� (26)
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][spawn_processes] Failed to execvp() '/scratch/0004/iplant/rogerab/job-0001431539033040-5056a550b8-0001-007-60eb1ec2-3ace-4d2a-b376-7194958dc7ca_0001/GeneSeqerMPI': ��� (26)
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][spawn_processes] Failed to execvp() '/scratch/0004/iplant/rogerab/job-0001431539033040-5056a550b8-0001-007-60eb1ec2-3ace-4d2a-b376-7194958dc7ca_0001/GeneSeqerMPI': ��� (26)
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][spawn_processes] Failed to execvp() '/scratch/0004/iplant/rogerab/job-0001431539033040-5056a550b8-0001-007-60eb1ec2-3ace-4d2a-b376-7194958dc7ca_0001/GeneSeqerMPI': �%� (26)
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][spawn_processes] Failed to execvp() '/scratch/0004/iplant/rogerab/job-0001431539033040-5056a550b8-0001-007-60eb1ec2-3ace-4d2a-b376-7194958dc7ca_0001/GeneSeqerMPI': �%� (26)
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][spawn_processes] Failed to execvp() '/scratch/0004/iplant/rogerab/job-0001431539033040-5056a550b8-0001-007-60eb1ec2-3ace-4d2a-b376-7194958dc7ca_0001/GeneSeqerMPI': ��� (26)
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][spawn_processes] Failed to execvp() '/scratch/0004/iplant/rogerab/job-0001431539033040-5056a550b8-0001-007-60eb1ec2-3ace-4d2a-b376-7194958dc7ca_0001/GeneSeqerMPI': �%� (26)
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][spawn_processes] Failed to execvp() '/scratch/0004/iplant/rogerab/job-0001431539033040-5056a550b8-0001-007-60eb1ec2-3ace-4d2a-b376-7194958dc7ca_0001/GeneSeqerMPI': �%� (26)
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][spawn_processes] Failed to execvp() '/scratch/0004/iplant/rogerab/job-0001431539033040-5056a550b8-0001-007-60eb1ec2-3ace-4d2a-b376-7194958dc7ca_0001/GeneSeqerMPI': �%� (26)
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][spawn_processes] Failed to execvp() '/scratch/0004/iplant/rogerab/job-0001431539033040-5056a550b8-0001-007-60eb1ec2-3ace-4d2a-b376-7194958dc7ca_0001/GeneSeqerMPI': �%� (26)
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][spawn_processes] Failed to execvp() '/scratch/0004/iplant/rogerab/job-0001431539033040-5056a550b8-0001-007-60eb1ec2-3ace-4d2a-b376-7194958dc7ca_0001/GeneSeqerMPI': �%� (26)
[c426-202.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI process (rank: 1, pid: 90
etc,etc,etc,etc
--
Roger Barthelson Ph.D.
Scientific Analyst
iPlant Collaborative
BIO5 Institute, University of Arizona
Phone: 520-977-5249
Email: rogerab at email.arizona.edu<mailto:rogerab at email.arizona.edu>
Web: www.iplantcollaborative.org/<http://www.iplantcollaborative.org/>
_______________________________________________
Iplant-api-dev Mailing List: Iplant-api-dev at iplantcollaborative.org<mailto:Iplant-api-dev at iplantcollaborative.org>
List Info and Archives: http://mail.iplantcollaborative.org/mailman/listinfo/iplant-api-dev
One-click Unsubscribe: http://mail.iplantcollaborative.org/mailman/options/iplant-api-dev/dooley%40tacc.utexas.edu?unsub=1&unsubconfirm=1
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.iplantcollaborative.org/pipermail/iplant-api-dev/attachments/20150519/ee1e718b/attachment-0001.html
More information about the Iplant-api-dev
mailing list