From anne.campagna at partners.basf.com Wed Feb 3 03:35:23 2021 From: anne.campagna at partners.basf.com (Anne Campagna) Date: Wed, 03 Feb 2021 10:35:23 -0000 Subject: [maker-devel] maker error with fully masked sequence Message-ID: Dear Maker Developers, I am running Maker v2.31, with proteomes, rnaseq, repeat library and fgenesh. I came across the following error (please note I change the path names due to confidentiality) running fgenesh. #--------- command -------------# Widget::fgenesh: /maker_path1/maker/2.31.10/bin/../fgenesh_path/fgenesh/8.0.0a/fgenesh /tools/bioinfo/app/fgenesh-2.6/fgenesh_model_file /maker_output_path/run_02/tmp/maker_l129tl/0/14_0.42724263-42725212.Dicots.auto_annotator.fgenesh.fasta -exon_table:/ maker_output_path/run_02/tmp/maker_l129tl/0/14_0.42724263-42725212.Dicots.auto_annotator.xdef.fgenesh > / maker_output_path /run_02/tmp/maker_l129tl/0/14_0.42724263-42725212.Dicots.auto_annotator.fgenesh #-------------------------------# ERROR: FgenesH failed --> rank=NA, hostname=by0q4y.eu.seeds.basf.net ERROR: Failed while annotating transcripts ERROR: Chunk failed at level:1, tier_type:4 FAILED CONTIG:chrC03 ERROR: Chunk failed at level:6, tier_type:0 FAILED CONTIG:chrC03 I then looked at the fasta file for this particular chunk (see below) and the error seems to be due to that chunk being fully masked. What would be the workaround for this so that maker can handle this and doesn't fail the whole contig/chromosome? $more 14_0.42724263-42725212.Dicots.auto_annotator.fgenesh.fasta >chrC03 14_0 offset:42724263 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Thanks a lot for your help! Anne -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.eylenbosch at partners.basf.com Tue Feb 23 03:13:27 2021 From: thomas.eylenbosch at partners.basf.com (Thomas Eylenbosch) Date: Tue, 23 Feb 2021 10:13:27 -0000 Subject: [maker-devel] maker/openmpi multiple jobs dont "see" each other Message-ID: Hello We are trying to run a maker job with the combination of openmpi. And we are using the following qsub script #!/bin/bash ## SGE settings #$ -N j_maker_20210204_112200_53455 #$ -pe openmpi 8 #$ -o log.out #$ -e log.err #$ -M campaga2 #$ -hard #$ -q main.largemem,main.regular #$ -l vf=6.250G,h_rss=55G ## ... # Run the command mpiexec -n 8 \ $installpath/maker "maker_opts.ctl" "maker_bopts.ctl" "maker_exe.ctl" But we receive the following error: it seems that the multiple jobs dont "see" each other which cause the following message --Next Contig-- #--------------------------------------------------------------------- Another instance of maker is processing this contig!! SeqID: chrA10 Length: 17398227 #--------------------------------------------------------------------- Which is probably related with the following topic: http://gmod.827538.n3.nabble.com/Does-maker-support-muti-processing-for-a-single-long-fasta-sequence-using-openMPI-td4061342.html maker is installed with the openmpi options, and our openmpi software is correctly installed I have downloaded this example: https://raw.githubusercontent.com/open-mpi/ompi/master/examples/hello_c.c And I build it and run it, and it seems openmpi is correctly installed. piexec --mca btl ^openib -N 5 ./hello_c Hello, world, I am 0 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 1 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 3 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 4 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 2 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) It is displaying 5 different lines (rank 0 to 4 of 5). Could you help us with the "Another instance of maker is processing this contig" error message ? Best regards / met vriendelijke groeten Thomas Eylenbosch DevOps Engineer (OnSite), Gluo N.V. Currently available at BASF Belgium Coordination Center CommV Email: thomas.eylenbosch at partners.basf.com Postal Address: BASF Belgium Coordination Center CommV, Technologiepark 101, 9052 Gent Zwijnaarde, Belgium BASF Belgium Coordination Center CommV Scheldelaan 600, 2040 Antwerpen, Belgi? RPR Antwerpen (afd. Antwerpen) BTW BE0862.390.376 www.basf.be Deutsche Bank AG IBAN: BE43 8262 8044 4801 BIC: DEUTBEBE Information on data protection can be found here: https://www.basf.com/global/en/legal/data-protection-at-basf.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.eylenbosch at partners.basf.com Fri Feb 26 01:29:21 2021 From: thomas.eylenbosch at partners.basf.com (Thomas Eylenbosch) Date: Fri, 26 Feb 2021 08:29:21 +0000 Subject: [maker-devel] maker/openmpi multiple jobs dont "see" each other Message-ID: Hello My apologies if this email has been received twice, but it seems I was not accepted yet for the mailing list. We are trying to run a maker job with the combination of openmpi. And we are using the following qsub script #!/bin/bash ## SGE settings #$ -N j_maker_20210204_112200_53455 #$ -pe openmpi 8 #$ -o log.out #$ -e log.err #$ -M campaga2 #$ -hard #$ -q main.largemem,main.regular #$ -l vf=6.250G,h_rss=55G ## ... # Run the command mpiexec -n 8 \ $installpath/maker "maker_opts.ctl" "maker_bopts.ctl" "maker_exe.ctl" But we receive the following error: it seems that the multiple jobs dont "see" each other which cause the following message --Next Contig-- #--------------------------------------------------------------------- Another instance of maker is processing this contig!! SeqID: chrA10 Length: 17398227 #--------------------------------------------------------------------- Which is probably related with the following topic: http://gmod.827538.n3.nabble.com/Does-maker-support-muti-processing-for-a-single-long-fasta-sequence-using-openMPI-td4061342.html maker is installed with the openmpi options, and our openmpi software is correctly installed I have downloaded this example: https://raw.githubusercontent.com/open-mpi/ompi/master/examples/hello_c.c And I build it and run it, and it seems openmpi is correctly installed. piexec --mca btl ^openib -N 5 ./hello_c Hello, world, I am 0 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 1 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 3 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 4 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 2 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) It is displaying 5 different lines (rank 0 to 4 of 5). Could you help us with the "Another instance of maker is processing this contig" error message ? Best regards / met vriendelijke groeten Thomas Eylenbosch DevOps Engineer (OnSite), Gluo N.V. Currently available at BASF Belgium Coordination Center CommV Email: thomas.eylenbosch at partners.basf.com Postal Address: BASF Belgium Coordination Center CommV, Technologiepark 101, 9052 Gent Zwijnaarde, Belgium BASF Belgium Coordination Center CommV Scheldelaan 600, 2040 Antwerpen, Belgi? RPR Antwerpen (afd. Antwerpen) BTW BE0862.390.376 www.basf.be Deutsche Bank AG IBAN: BE43 8262 8044 4801 BIC: DEUTBEBE Information on data protection can be found here: https://www.basf.com/global/en/legal/data-protection-at-basf.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From anne.campagna at partners.basf.com Wed Feb 3 03:35:23 2021 From: anne.campagna at partners.basf.com (Anne Campagna) Date: Wed, 03 Feb 2021 10:35:23 -0000 Subject: [maker-devel] maker error with fully masked sequence Message-ID: Dear Maker Developers, I am running Maker v2.31, with proteomes, rnaseq, repeat library and fgenesh. I came across the following error (please note I change the path names due to confidentiality) running fgenesh. #--------- command -------------# Widget::fgenesh: /maker_path1/maker/2.31.10/bin/../fgenesh_path/fgenesh/8.0.0a/fgenesh /tools/bioinfo/app/fgenesh-2.6/fgenesh_model_file /maker_output_path/run_02/tmp/maker_l129tl/0/14_0.42724263-42725212.Dicots.auto_annotator.fgenesh.fasta -exon_table:/ maker_output_path/run_02/tmp/maker_l129tl/0/14_0.42724263-42725212.Dicots.auto_annotator.xdef.fgenesh > / maker_output_path /run_02/tmp/maker_l129tl/0/14_0.42724263-42725212.Dicots.auto_annotator.fgenesh #-------------------------------# ERROR: FgenesH failed --> rank=NA, hostname=by0q4y.eu.seeds.basf.net ERROR: Failed while annotating transcripts ERROR: Chunk failed at level:1, tier_type:4 FAILED CONTIG:chrC03 ERROR: Chunk failed at level:6, tier_type:0 FAILED CONTIG:chrC03 I then looked at the fasta file for this particular chunk (see below) and the error seems to be due to that chunk being fully masked. What would be the workaround for this so that maker can handle this and doesn't fail the whole contig/chromosome? $more 14_0.42724263-42725212.Dicots.auto_annotator.fgenesh.fasta >chrC03 14_0 offset:42724263 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Thanks a lot for your help! Anne -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.eylenbosch at partners.basf.com Tue Feb 23 03:13:27 2021 From: thomas.eylenbosch at partners.basf.com (Thomas Eylenbosch) Date: Tue, 23 Feb 2021 10:13:27 -0000 Subject: [maker-devel] maker/openmpi multiple jobs dont "see" each other Message-ID: Hello We are trying to run a maker job with the combination of openmpi. And we are using the following qsub script #!/bin/bash ## SGE settings #$ -N j_maker_20210204_112200_53455 #$ -pe openmpi 8 #$ -o log.out #$ -e log.err #$ -M campaga2 #$ -hard #$ -q main.largemem,main.regular #$ -l vf=6.250G,h_rss=55G ## ... # Run the command mpiexec -n 8 \ $installpath/maker "maker_opts.ctl" "maker_bopts.ctl" "maker_exe.ctl" But we receive the following error: it seems that the multiple jobs dont "see" each other which cause the following message --Next Contig-- #--------------------------------------------------------------------- Another instance of maker is processing this contig!! SeqID: chrA10 Length: 17398227 #--------------------------------------------------------------------- Which is probably related with the following topic: http://gmod.827538.n3.nabble.com/Does-maker-support-muti-processing-for-a-single-long-fasta-sequence-using-openMPI-td4061342.html maker is installed with the openmpi options, and our openmpi software is correctly installed I have downloaded this example: https://raw.githubusercontent.com/open-mpi/ompi/master/examples/hello_c.c And I build it and run it, and it seems openmpi is correctly installed. piexec --mca btl ^openib -N 5 ./hello_c Hello, world, I am 0 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 1 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 3 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 4 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 2 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) It is displaying 5 different lines (rank 0 to 4 of 5). Could you help us with the "Another instance of maker is processing this contig" error message ? Best regards / met vriendelijke groeten Thomas Eylenbosch DevOps Engineer (OnSite), Gluo N.V. Currently available at BASF Belgium Coordination Center CommV Email: thomas.eylenbosch at partners.basf.com Postal Address: BASF Belgium Coordination Center CommV, Technologiepark 101, 9052 Gent Zwijnaarde, Belgium BASF Belgium Coordination Center CommV Scheldelaan 600, 2040 Antwerpen, Belgi? RPR Antwerpen (afd. Antwerpen) BTW BE0862.390.376 www.basf.be Deutsche Bank AG IBAN: BE43 8262 8044 4801 BIC: DEUTBEBE Information on data protection can be found here: https://www.basf.com/global/en/legal/data-protection-at-basf.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.eylenbosch at partners.basf.com Fri Feb 26 01:29:21 2021 From: thomas.eylenbosch at partners.basf.com (Thomas Eylenbosch) Date: Fri, 26 Feb 2021 08:29:21 +0000 Subject: [maker-devel] maker/openmpi multiple jobs dont "see" each other Message-ID: Hello My apologies if this email has been received twice, but it seems I was not accepted yet for the mailing list. We are trying to run a maker job with the combination of openmpi. And we are using the following qsub script #!/bin/bash ## SGE settings #$ -N j_maker_20210204_112200_53455 #$ -pe openmpi 8 #$ -o log.out #$ -e log.err #$ -M campaga2 #$ -hard #$ -q main.largemem,main.regular #$ -l vf=6.250G,h_rss=55G ## ... # Run the command mpiexec -n 8 \ $installpath/maker "maker_opts.ctl" "maker_bopts.ctl" "maker_exe.ctl" But we receive the following error: it seems that the multiple jobs dont "see" each other which cause the following message --Next Contig-- #--------------------------------------------------------------------- Another instance of maker is processing this contig!! SeqID: chrA10 Length: 17398227 #--------------------------------------------------------------------- Which is probably related with the following topic: http://gmod.827538.n3.nabble.com/Does-maker-support-muti-processing-for-a-single-long-fasta-sequence-using-openMPI-td4061342.html maker is installed with the openmpi options, and our openmpi software is correctly installed I have downloaded this example: https://raw.githubusercontent.com/open-mpi/ompi/master/examples/hello_c.c And I build it and run it, and it seems openmpi is correctly installed. piexec --mca btl ^openib -N 5 ./hello_c Hello, world, I am 0 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 1 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 3 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 4 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 2 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) It is displaying 5 different lines (rank 0 to 4 of 5). Could you help us with the "Another instance of maker is processing this contig" error message ? Best regards / met vriendelijke groeten Thomas Eylenbosch DevOps Engineer (OnSite), Gluo N.V. Currently available at BASF Belgium Coordination Center CommV Email: thomas.eylenbosch at partners.basf.com Postal Address: BASF Belgium Coordination Center CommV, Technologiepark 101, 9052 Gent Zwijnaarde, Belgium BASF Belgium Coordination Center CommV Scheldelaan 600, 2040 Antwerpen, Belgi? RPR Antwerpen (afd. Antwerpen) BTW BE0862.390.376 www.basf.be Deutsche Bank AG IBAN: BE43 8262 8044 4801 BIC: DEUTBEBE Information on data protection can be found here: https://www.basf.com/global/en/legal/data-protection-at-basf.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From anne.campagna at partners.basf.com Wed Feb 3 03:35:23 2021 From: anne.campagna at partners.basf.com (Anne Campagna) Date: Wed, 03 Feb 2021 10:35:23 -0000 Subject: [maker-devel] maker error with fully masked sequence Message-ID: Dear Maker Developers, I am running Maker v2.31, with proteomes, rnaseq, repeat library and fgenesh. I came across the following error (please note I change the path names due to confidentiality) running fgenesh. #--------- command -------------# Widget::fgenesh: /maker_path1/maker/2.31.10/bin/../fgenesh_path/fgenesh/8.0.0a/fgenesh /tools/bioinfo/app/fgenesh-2.6/fgenesh_model_file /maker_output_path/run_02/tmp/maker_l129tl/0/14_0.42724263-42725212.Dicots.auto_annotator.fgenesh.fasta -exon_table:/ maker_output_path/run_02/tmp/maker_l129tl/0/14_0.42724263-42725212.Dicots.auto_annotator.xdef.fgenesh > / maker_output_path /run_02/tmp/maker_l129tl/0/14_0.42724263-42725212.Dicots.auto_annotator.fgenesh #-------------------------------# ERROR: FgenesH failed --> rank=NA, hostname=by0q4y.eu.seeds.basf.net ERROR: Failed while annotating transcripts ERROR: Chunk failed at level:1, tier_type:4 FAILED CONTIG:chrC03 ERROR: Chunk failed at level:6, tier_type:0 FAILED CONTIG:chrC03 I then looked at the fasta file for this particular chunk (see below) and the error seems to be due to that chunk being fully masked. What would be the workaround for this so that maker can handle this and doesn't fail the whole contig/chromosome? $more 14_0.42724263-42725212.Dicots.auto_annotator.fgenesh.fasta >chrC03 14_0 offset:42724263 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Thanks a lot for your help! Anne -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.eylenbosch at partners.basf.com Tue Feb 23 03:13:27 2021 From: thomas.eylenbosch at partners.basf.com (Thomas Eylenbosch) Date: Tue, 23 Feb 2021 10:13:27 -0000 Subject: [maker-devel] maker/openmpi multiple jobs dont "see" each other Message-ID: Hello We are trying to run a maker job with the combination of openmpi. And we are using the following qsub script #!/bin/bash ## SGE settings #$ -N j_maker_20210204_112200_53455 #$ -pe openmpi 8 #$ -o log.out #$ -e log.err #$ -M campaga2 #$ -hard #$ -q main.largemem,main.regular #$ -l vf=6.250G,h_rss=55G ## ... # Run the command mpiexec -n 8 \ $installpath/maker "maker_opts.ctl" "maker_bopts.ctl" "maker_exe.ctl" But we receive the following error: it seems that the multiple jobs dont "see" each other which cause the following message --Next Contig-- #--------------------------------------------------------------------- Another instance of maker is processing this contig!! SeqID: chrA10 Length: 17398227 #--------------------------------------------------------------------- Which is probably related with the following topic: http://gmod.827538.n3.nabble.com/Does-maker-support-muti-processing-for-a-single-long-fasta-sequence-using-openMPI-td4061342.html maker is installed with the openmpi options, and our openmpi software is correctly installed I have downloaded this example: https://raw.githubusercontent.com/open-mpi/ompi/master/examples/hello_c.c And I build it and run it, and it seems openmpi is correctly installed. piexec --mca btl ^openib -N 5 ./hello_c Hello, world, I am 0 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 1 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 3 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 4 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 2 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) It is displaying 5 different lines (rank 0 to 4 of 5). Could you help us with the "Another instance of maker is processing this contig" error message ? Best regards / met vriendelijke groeten Thomas Eylenbosch DevOps Engineer (OnSite), Gluo N.V. Currently available at BASF Belgium Coordination Center CommV Email: thomas.eylenbosch at partners.basf.com Postal Address: BASF Belgium Coordination Center CommV, Technologiepark 101, 9052 Gent Zwijnaarde, Belgium BASF Belgium Coordination Center CommV Scheldelaan 600, 2040 Antwerpen, Belgi? RPR Antwerpen (afd. Antwerpen) BTW BE0862.390.376 www.basf.be Deutsche Bank AG IBAN: BE43 8262 8044 4801 BIC: DEUTBEBE Information on data protection can be found here: https://www.basf.com/global/en/legal/data-protection-at-basf.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.eylenbosch at partners.basf.com Fri Feb 26 01:29:21 2021 From: thomas.eylenbosch at partners.basf.com (Thomas Eylenbosch) Date: Fri, 26 Feb 2021 08:29:21 +0000 Subject: [maker-devel] maker/openmpi multiple jobs dont "see" each other Message-ID: Hello My apologies if this email has been received twice, but it seems I was not accepted yet for the mailing list. We are trying to run a maker job with the combination of openmpi. And we are using the following qsub script #!/bin/bash ## SGE settings #$ -N j_maker_20210204_112200_53455 #$ -pe openmpi 8 #$ -o log.out #$ -e log.err #$ -M campaga2 #$ -hard #$ -q main.largemem,main.regular #$ -l vf=6.250G,h_rss=55G ## ... # Run the command mpiexec -n 8 \ $installpath/maker "maker_opts.ctl" "maker_bopts.ctl" "maker_exe.ctl" But we receive the following error: it seems that the multiple jobs dont "see" each other which cause the following message --Next Contig-- #--------------------------------------------------------------------- Another instance of maker is processing this contig!! SeqID: chrA10 Length: 17398227 #--------------------------------------------------------------------- Which is probably related with the following topic: http://gmod.827538.n3.nabble.com/Does-maker-support-muti-processing-for-a-single-long-fasta-sequence-using-openMPI-td4061342.html maker is installed with the openmpi options, and our openmpi software is correctly installed I have downloaded this example: https://raw.githubusercontent.com/open-mpi/ompi/master/examples/hello_c.c And I build it and run it, and it seems openmpi is correctly installed. piexec --mca btl ^openib -N 5 ./hello_c Hello, world, I am 0 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 1 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 3 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 4 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 2 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) It is displaying 5 different lines (rank 0 to 4 of 5). Could you help us with the "Another instance of maker is processing this contig" error message ? Best regards / met vriendelijke groeten Thomas Eylenbosch DevOps Engineer (OnSite), Gluo N.V. Currently available at BASF Belgium Coordination Center CommV Email: thomas.eylenbosch at partners.basf.com Postal Address: BASF Belgium Coordination Center CommV, Technologiepark 101, 9052 Gent Zwijnaarde, Belgium BASF Belgium Coordination Center CommV Scheldelaan 600, 2040 Antwerpen, Belgi? RPR Antwerpen (afd. Antwerpen) BTW BE0862.390.376 www.basf.be Deutsche Bank AG IBAN: BE43 8262 8044 4801 BIC: DEUTBEBE Information on data protection can be found here: https://www.basf.com/global/en/legal/data-protection-at-basf.html -------------- next part -------------- An HTML attachment was scrubbed... URL: