[Iplant-api-dev] Odd Failures of Public Apps

Rion Dooley dooley at tacc.utexas.edu
Tue May 19 14:08:45 MST 2015

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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/>
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