Question: Error while abyss running on cluster
0
gravatar for caizexi123
4.0 years ago by
caizexi12350
Denmark
caizexi12350 wrote:

Hi, guys!

I am running Abyss on cluster, I compiled the Abyss-1.5.2 with the OpenMPI-1.4.3 the server provided on my director on one of the nod.

I compiled completed, and there is Abyss-P in the installed director.

Then I submit my job via LSF system:

APP_NAME=bioloong

NP=10

RUN="/share/home/jinlab/bin/bin/abyss-pe k=50 name=coix in='/share/home/jinlab/data/test/coix_1.fastq'"

 

But the job was killed, with the LSF output:

Sender: LSF System <lsfadmin1@blade115>
Subject: Job 481296: <testjob> Exited

Job <testjob> was submitted from host <bio-login2> by user <jinlab> in cluster <bcc_cloud1>.
Job was executed on host(s) <10*blade115>, in queue <bioloong>, as user <jinlab> in cluster <bcc_cloud1>.
</share/home/jinlab> was used as the home directory.
</share/home/jinlab/data/test> was used as the working directory.
Started at Sun Mar 22 17:03:51 2015
Results reported at Sun Mar 22 17:15:29 2015

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
testjob
------------------------------------------------------------

Exited with exit code 2.

Resource usage summary:

    CPU time   :      1.10 sec.
    Max Memory :        65 MB
    Max Swap   :       603 MB

    Max Processes  :        36
    Max Threads    :        44

The output (if any) follows:

RUN=/share/home/jinlab/bin/bin/abyss-pe k=50 name=coix in='/share/home/jinlab/data/test/coix_1.fastq'
/lsf1/8.0/linux2.6-glibc2.3-x86_64/bin/mpirun.lsf -np 10 ABYSS-P -k50 -q3   --coverage-hist=coverage.hist -s coix-bubbles.fa  -o coix-1.fa /share/home/jinlab/data/test/coix_1.fastq 
...
/lsf1/8.0/linux2.6-glibc2.3-x86_64/bin/mpirun.lsf -np 10 ABYSS-P -k50 -q3   --coverage-hist=coverage.hist -s coix-bubbles.fa  -o coix-1.fa /share/home/jinlab/data/test/coix_1.fastq 
--------------------------------------------------------------------------
mpirun could not find anything to do.

It is possible that you forgot to specify how many processes to run
via the "-np" argument.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun could not find anything to do.

It is possible that you forgot to specify how many processes to run
via the "-np" argument.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun could not find anything to do.

It is possible that you forgot to specify how many processes to run
via the "-np" argument.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun could not find anything to do.

It is possible that you forgot to specify how many processes to run
via the "-np" argument.
--------------------------------------------------------------------------
[blade115:26042] [[7220,1],1] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 105
[blade115:26042] [[7220,1],1] could not get route to [[INVALID],INVALID]
[...
[blade115:26051] [[7220,1],9] could not get route to [[INVALID],INVALID]
[blade115:26051] [[7220,1],9] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file base/plm_base_proxy.c at line 86
Job  /lsf1/8.0/linux2.6-glibc2.3-x86_64/bin/openmpi_wrapper -np 10 ABYSS-P -k50 -q3 --coverage-hist=coverage.hist -s coix-bubbles.fa -o coix-1.fa /share/home/jinlab/data/test/coix_1.fastq

TID   HOST_NAME   COMMAND_LINE            STATUS            TERMINATION_TIME
===== ========== ================  =======================  ===================
00001 blade115                     Undefined               
...
00010 blade115                     Undefined               
make: *** [coix-1.fa] 错误 1
Job  /lsf1/8.0/linux2.6-glibc2.3-x86_64/bin/openmpi_wrapper -np 10 ABYSS-P -k50 -q3 --coverage-hist=coverage.hist -s coix-bubbles.fa -o coix-1.fa /share/home/jinlab/data/test/coix_1.fastq

TID   HOST_NAME   COMMAND_LINE            STATUS            TERMINATION_TIME
===== ========== ================  =======================  ===================
00001 blade115                     Undefined               
...       
00010 blade115                     Undefined               
make: *** [coix-1.fa] 错误 1
Job  /lsf1/8.0/linux2.6-glibc2.3-x86_64/bin/openmpi_wrapper -np 10 ABYSS-P -k50 -q3 --coverage-hist=coverage.hist -s coix-bubbles.fa -o coix-1.fa /share/home/jinlab/data/test/coix_1.fastq

TID   HOST_NAME   COMMAND_LINE            STATUS            TERMINATION_TIME
===== ========== ================  =======================  ===================
00001 blade115                     Undefined               
...       
00010 blade115                     Undefined               
make: *** [coix-1.fa] 错误 1
make: *** [coix-1.fa] 错误 1
Job  /lsf1/8.0/linux2.6-glibc2.3-x86_64/bin/openmpi_wrapper -np 10 ABYSS-P -k50 -q3 --coverage-hist=coverage.hist -s coix-bubbles.fa -o coix-1.fa /share/home/jinlab/data/test/coix_1.fastq

TID   HOST_NAME   COMMAND_LINE            STATUS            TERMINATION_TIME
===== ========== ================  =======================  ===================
00001 blade115                     Undefined               
...          
00010 blade115                     Undefined               
Mar 22 17:04:14 2015 25906 7 8.0.1 reportJRusage: failed to send rusage report to SBD
Mar 22 17:08:53 2015 25988 4 8.0.1 checkPJLStartup: PAM has received no feedback from any TaskStarter for 300 seconds after PJL has started. Shutting down the job ...
...
Mar 22 17:08:53 2015 25986 4 8.0.1 checkPJLStartup: PAM has received no feedback from any TaskStarter for 300 seconds after PJL has started. Shutting down the job ...
Mar 22 17:14:13 2015 25906 Last message repeated 574 time(s).
Mar 22 17:14:14 2015 25906 7 8.0.1 reportJRusage: failed to send rusage report to SBD
Mar 22 17:14:56 2015 25988 3 8.0.1 PAM: waitForPJLExit: Timed out while waiting for PJL to exit. Sending SIGKILL
Job  /lsf1/8.0/linux2.6-glibc2.3-x86_64/bin/openmpi_wrapper -np 10 ABYSS-P -k50 -q3 --coverage-hist=coverage.hist -s coix-bubbles.fa -o coix-1.fa /share/home/jinlab/data/test/coix_1.fastq

TID   HOST_NAME   COMMAND_LINE            STATUS            TERMINATION_TIME
===== ========== ================  =======================  ===================
00001 blade115                     Undefined               
...   
00010 blade115                     Undefined               
make: *** [coix-1.fa] 已杀死
Mar 22 17:14:59 2015 25992 3 8.0.1 PAM: waitForPJLExit: Timed out while waiting for PJL to exit. Sending SIGKILL
Job  /lsf1/8.0/linux2.6-glibc2.3-x86_64/bin/openmpi_wrapper -np 10 ABYSS-P -k50 -q3 --coverage-hist=coverage.hist -s coix-bubbles.fa -o coix-1.fa /share/home/jinlab/data/test/coix_1.fastq

TID   HOST_NAME   COMMAND_LINE            STATUS            TERMINATION_TIME
===== ========== ================  =======================  ===================
00001 blade115                     Undefined               
...      
00010 blade115                     Undefined               
make: *** [coix-1.fa] 已杀死
Mar 22 17:15:02 2015 25989 3 8.0.1 PAM: waitForPJLExit: Timed out while waiting for PJL to exit. Sending SIGKILL
Job  /lsf1/8.0/linux2.6-glibc2.3-x86_64/bin/openmpi_wrapper -np 10 ABYSS-P -k50 -q3 --coverage-hist=coverage.hist -s coix-bubbles.fa -o coix-1.fa /share/home/jinlab/data/test/coix_1.fastq

TID   HOST_NAME   COMMAND_LINE            STATUS            TERMINATION_TIME
===== ========== ================  =======================  ===================
00001 blade115                     Undefined               
...
00010 blade115                     Undefined               
make: *** [coix-1.fa] 已杀死
Mar 22 17:15:06 2015 25987 3 8.0.1 PAM: waitForPJLExit: Timed out while waiting for PJL to exit. Sending SIGKILL
Job  /lsf1/8.0/linux2.6-glibc2.3-x86_64/bin/openmpi_wrapper -np 10 ABYSS-P -k50 -q3 --coverage-hist=coverage.hist -s coix-bubbles.fa -o coix-1.fa /share/home/jinlab/data/test/coix_1.fastq

TID   HOST_NAME   COMMAND_LINE            STATUS            TERMINATION_TIME
===== ========== ================  =======================  ===================
00001 blade115                     Undefined               
...
00010 blade115                     Undefined               
make: *** [coix-1.fa] 已杀死
Mar 22 17:15:26 2015 25984 3 8.0.1 PAM: waitForPJLExit: Timed out while waiting for PJL to exit. Sending SIGKILL
Job  /lsf1/8.0/linux2.6-glibc2.3-x86_64/bin/openmpi_wrapper -np 10 ABYSS-P -k50 -q3 --coverage-hist=coverage.hist -s coix-bubbles.fa -o coix-1.fa /share/home/jinlab/data/test/coix_1.fastq

TID   HOST_NAME   COMMAND_LINE            STATUS            TERMINATION_TIME
===== ========== ================  =======================  ===================
00001 blade115                     Undefined               
...
00010 blade115                     Undefined               
make: *** [coix-1.fa] 已杀死
Mar 22 17:15:26 2015 25986 3 8.0.1 PAM: waitForPJLExit: Timed out while waiting for PJL to exit. Sending SIGKILL
Job  /lsf1/8.0/linux2.6-glibc2.3-x86_64/bin/openmpi_wrapper -np 10 ABYSS-P -k50 -q3 --coverage-hist=coverage.hist -s coix-bubbles.fa -o coix-1.fa /share/home/jinlab/data/test/coix_1.fastq

TID   HOST_NAME   COMMAND_LINE            STATUS            TERMINATION_TIME
===== ========== ================  =======================  ===================
00001 blade115                     Undefined               
...
00010 blade115                     Undefined               
make: *** [coix-1.fa] 已杀死
Job  /lsf1/8.0/linux2.6-glibc2.3-x86_64/bin/openmpi_wrapper /share/home/jinlab/bin/bin/abyss-pe k=50 name=coix in=/share/home/jinlab/data/test/coix_1.fastq

TID   HOST_NAME   COMMAND_LINE            STATUS            TERMINATION_TIME
===== ========== ================  =======================  ===================
00000 blade115   /share/home/jinl  Exit (2)                 03/22/2015 17:15:06
...
00009 blade115   /share/home/jinl  Exit (2)                 03/22/2015 17:15:2

 

Anyone knows what's wrong?

 

abyss tool assembly • 2.1k views
ADD COMMENTlink modified 4.0 years ago by Pierre Lindenbaum118k • written 4.0 years ago by caizexi12350

I'm afraid that those error messages don't mean much to me. They look pretty specific to LSF, which I haven't used. Sorry I couldn't be of more help.

ADD REPLYlink written 4.0 years ago by Shaun Jackman420

I can't tell what the problem is either, unfortunately.

Have you successfully run MPI jobs on your cluster before? If not, I would suggest compiling and testing with a simple MPI "Hello, World!" program, such as the one provided here: http://mpitutorial.com/tutorials/mpi-hello-world/.  That would let you know whether the problem is specific to ABySS or if it is a problem with the job submission parameters.

ADD REPLYlink written 4.0 years ago by benv710
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