[Iplant-api-dev] Odd Failures of Public Apps
Barthelson, Roger A - (rogerab)
rogerab at email.arizona.edu
Tue May 19 14:04:51 MST 2015
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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