Satsuma2 dies with Segmentation fault (core dumped) #21
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Hi Claudia, |
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Hi Jon,
The output files at this point are kmer files 11,13,15,17,19,21 etc. up to 31 and a "satsuma.log" file which just says "Starting". The way it has been set up on the cluster/HPC here is I need to add the modules each time. Do you think the way it has been installed could be the issue? When I run the test data I get this which is the same error. Thank you for your help! |
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Error in binding sounds like a network error. Do you have permissions to open ports and such?
Best,
bj
… On 6 Nov 2019, at 10:50, claudiamartin94 ***@***.***> wrote:
Hi Jon,
Thanks for commenting so quickly!
The job doesn't fail immediately when I run the script above or the test script, and they both have the same error. It manages to sort the Kmer array (and I get output files such as kmatch_results.k15). It loads both of the fasta sequences. It displays an "error on binding" but then seems to continue.
Then it collects forward and reverse matches and creates query chunks.
Just before it fails it says
"Loading target sequence: /gpfs/home/yuw17aeu/satsuma/dog.X.part.fasta
Creating target chunks...
select=0 chunks=82
chunks: 82
DONE
TIME SPENT ON LOADING: 1
== launching workers ==
== Entering communication loop ==
comm loop for e0003 3495
worker created, now to work!!!
worker created, now to work!!!
Segmentation fault (core dumped)"
The output files at this point are kmer files 11,13,15,17,19,21 etc. up to 31 and a "satsuma.log" file which just says "Starting".
The way it has been set up on the cluster/HPC here is I need to add the modules each time. Do you think the way it has been installed could be the issue?
When I run the test data I get this which is the same error.
== launching workers ==
== Entering communication loop ==
comm loop for e0078 3491
worker created, now to work!!!
worker created, now to work!!!
/gpfs/home/yuw17aeu/.lsbatch/1573037128.868135.shell: line 6: 26635 Segmentation fault (core dumped) SatsumaSynteny2 -q /gpfs/home/yuw17aeu/satsuma/human.X.part.fasta -t /gpfs/home/yuw17aeu/satsuma/dog.X.part.fasta -o /gpfs/home/yuw17aeu/satsuma/xcorr_sample_synt_jon -threads 2
Thank you for your help!
Claudia
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Hi Bernardo, I may ask the cluster to try and reinstall the program if you think that's the issue. When they initially installed it I was having trouble locating the path to the binaries. This is what they told me. "Satsuma2 has been installed on HPC as a singularity container image. The reason being it requires Gcc 5.5 and cmake 3.x which is not available on operating system we have (Centos 6). As such the binaries are part of satsuma2.sif (image file) and can not be accessed by user on HPC." Could you advise how is best to instruct the HPC group to install Satsuma. Best, |
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The network code is not necessarily super robust there, so a binding error may well trigger a segfault when trying to read from an invalid file descriptor or something like that.
If you attach a debugger to it it would be trivial to check if that is the case, although I have no clue if your setup allows that.
Best,
bj
… On 6 Nov 2019, at 11:36, claudiamartin94 ***@***.***> wrote:
Hi Bernardo,
I doubt I do, but I'm not sure that this is the same problem as the segmentation fault. Or maybe the binding error triggers problems in the segmentation step.
I may ask the cluster to try and reinstall the program if you think that's the issue. When they initially installed it I was having trouble locating the path to the binaries.
This is what they told me. "Satsuma2 has been installed on HPC as a singularity container image. The reason being it requires Gcc 5.5 and cmake 3.x which is not available on operating system we have (Centos 6). As such the binaries are part of satsuma2.sif (image file) and can not be accessed by user on HPC."
Could you advise how is best to instruct the HPC group to install Satsuma.
Best,
Claudia
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I'm afraid I don't understand what you are suggesting. Do you know of any other software that has similar capabilities? I need to map my bird genome scaffolds to the Zebra finch genome. Currently our genome is in many contigs and it's hard to visualise genome-wide patterns. Best, |
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You can try the old version of satsuma, which is slower but doesn’t use network-based communication but rather disk-based.
Manfred?
Best,
bj
… On 6 Nov 2019, at 11:45, claudiamartin94 ***@***.***> wrote:
I'm afraid I don't understand what you are suggesting.
It's unlikely that I am able to use a debugger as I don't have much control over the cluster. The HPC team don't know how to help so I'm a bit stuck.
Do you know of any other software that has similar capabilities? I need to map my bird genome scaffolds to the Zebra finch genome. Currently our genome is in many contigs and it's hard to visualise genome-wide patterns.
Best,
Claudia
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Hi Claudia,
What exactly is the issue (sorry if I missed some previous messages)? Running the old version of Satsuma might not be the best idea, especially on a distributed cluster, where there is a lot of latency in disk-based communication.
Cheers,
- Manfred
On 2019-11-06 16:07, Bernardo Clavijo wrote:
You can try the old version of satsuma, which is slower but doesn’t use network-based communication but rather disk-based.
Manfred?
Best,
bj
On 6 Nov 2019, at 11:45, claudiamartin94 <[email protected]<mailto:[email protected]>> wrote:
I'm afraid I don't understand what you are suggesting.
It's unlikely that I am able to use a debugger as I don't have much control over the cluster. The HPC team don't know how to help so I'm a bit stuck.
Do you know of any other software that has similar capabilities? I need to map my bird genome scaffolds to the Zebra finch genome. Currently our genome is in many contigs and it's hard to visualise genome-wide patterns.
Best,
Claudia
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Hi Manfred, Thank you for offering to help. I was having problems getting my own data to run so I have gone back to getting the practice data to work for the dog and human fasta files. When I run SatsumaSynteny2 on our HPC the job fails due to a Segmentation fault (see below for the error message). I have attempted with many variants of n. slaves, threads and mem. Are you aware of if there is anything I can do to get around this? == launching workers == == Entering communication loop == << output from stderr >> It's likely it could be a problem with how it has been installed on our cluster, but I'm unsure what to tell them that might help. Best, |
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The HPC team believe that its this line that causes the segmentation fault.. "/gpfs/software/satsuma2/3.1/bin/HomologyByXCorrSlave -master lgn02 -port 3494 -sid 1 -p 1 -q human.X.part.fasta -t dog.X.p art.fasta -l 0 -q_chunk 4096 -t_chunk 4096 -min_prob 0.99999 -cutoff 1.8 |
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Hi Claudia, |
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Hi Jon, |
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Hi Jon and Bernardo, The HPC team have updated our cluster now to Centos 7 and so I am trying to run SatsumaSynteny again. I appear to be missing the "satsuma_run.sh" file in the binary bin/ directory. Could this be a problem with the current configuration? I have the following files... BlockDisplaySatsuma ChromosomePaint HomologyByXCorr MatchDump MergeXCorrMatches ReverseSatsumaOut SatsumaToGFF Best, |
Hi,
I'm having trouble getting Satsuma to run even on the test dog and human sequences. I get the following segmentation error "/gpfs/home/yuw17aeu/.lsbatch/1572978474.862816.shell: line 15: 8112 Segmentation fault (core dumped) SatsumaSynteny2 -q /gpfs/home/yuw17aeu/satsuma/human.X.part.fasta -t /gpfs/home/yuw17aeu/satsuma/dog.X.part.fasta -o /gpfs/home/yuw17aeu/satsuma/xcorrtest -slaves 10 -threads 4"
My submission script is the following:
#/bin/sh
#BSUB -n 2
#BSUB -q long-eth
#BSUB -J satsuma-test
#BSUB -R "rusage[mem=10000]" -M 10000
#BSUB -oo satsuma-%J.out
#BSUB -ee satsuma-%J.err
. /etc/profile
module add satsuma2/3.1
module add singularity/3.1.1
export SATSUMA2_PATH=/gpfs/software/satsuma2/3.1/bin
SatsumaSynteny2 -q /gpfs/home/yuw17aeu/satsuma/human.X.part.fasta -t /gpfs/home/yuw17aeu/satsuma/dog.X.part.fasta -o /gpfs/home/yuw17aeu/satsuma/xcorrtest -slaves 10 -threads 4
Any help much appreciated,
thanks,
Claudia
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