Hi. Not really, I think. If you look here <https://www.biostars.org/p/63816/>, Ole introduces Gnu parallel and makes some example. One of these is the "*Blast on multiple machines*" example and here he shows how to run blast under GNU parallel first on the local node and then on multiple nodes.
I am trying to do the same stuff on our cluster so I have to submit that single parallel command with bsub. Anyhow I finally realized I can forget about blaunch and use simple ssh instead (blaunch is kerberos compliant but I don't need it outside afs partitions). g On Fri, Apr 17, 2015 at 4:20 PM, George Marselis <geo...@marsel.is> wrote: > Giuseppe, too much unformatted shell to figure out what is happening at a > glance. > > From what I can gather, you are using parallel to create scripts on > different nodes, which then get submitted to LSF on that node they were > created under. > > Am I right? > > On Thu, Apr 16, 2015 at 7:33 PM, Giuseppe Aprea <giuseppe.ap...@gmail.com> > wrote: > >> Hi, >> >> Maybe this time it could be a GNU parallel issue. >> >> I finally managed to run something with the following script: >> >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> #!/bin/bash >> >> >> #BSUB -J gnuParallel_blast_test # Name of the job. >> #BSUB -o %J.out # Appends std output to file >> %J.out. (%J is the Job ID) >> #BSUB -e %J.err # Appends std error to file >> %J.err. >> #BSUB -q cresco3_h144 # Queue name. >> #BSUB -n 8 # Number of CPUs. >> #BSUB -W 1210 # walltime >> >> module load 4.8.3/ncbi/12.0.0 >> module load 4.8.3/parallel/20150122 >> >> SLOTS=`cat ${LSB_DJOB_HOSTFILE} |wc -l` >> >> SERVER="" >> >> for i in `cat ${LSB_DJOB_HOSTFILE}| sort` >> do >> echo "/afs/enea.it/software/bin/blaunch.sh ${i}" >> servers >> done >> >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000 >> -query - > >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/all-vs-all-outfmt-6-filtered >> cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000.fasta >> | parallel --no-notice -vv -j ${SLOTS} --tmpdir >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp --wait >> --slf servers --block 20k --recstart '>' --pipe blastp -evalue 1e-05 >> -outfmt 6 -db >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000 >> -query - -out >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_{#} >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> >> The most important changes are >> >> - using --tmpdir options since temporary files must be on a shared >> filesystem(!!). >> - I used a larger data chunk (--block 20k instead of -N 1) >> - I used --wait for LSF load easing >> - I used {#} instead of {%} to tag result file for better debugging >> >> I finally got some non empty result files. Unfortunately I only got only >> 8 file of expected 22 >> >> these are stdout and stderr: >> >> >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par09c3l.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par09c3l.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par09c3l.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par09c3l.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par09c3l.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x003.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"3\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_3\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par26f1H.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par26f1H.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par26f1H.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par26f1H.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par26f1H.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x020.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"2\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_2\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/partdB11.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/partdB11.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/partdB11.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/partdB11.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/partdB11.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x020.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"5\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_5\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parzRBOV.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parzRBOV.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parzRBOV.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parzRBOV.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parzRBOV.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x020.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"8\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_8\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/pardYnbH.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/pardYnbH.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/pardYnbH.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/pardYnbH.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/pardYnbH.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x003.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"9\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_9\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parpLXXu.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parpLXXu.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parpLXXu.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parpLXXu.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parpLXXu.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x020.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"11\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_11\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parpDyze.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parpDyze.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parpDyze.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parpDyze.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parpDyze.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x003.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"12\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_12\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parska__.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parska__.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parska__.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parska__.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parska__.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x020.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"14\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_14\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par07hkH.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par07hkH.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par07hkH.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par07hkH.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par07hkH.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x003.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"15\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_15\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parwWxw0.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parwWxw0.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parwWxw0.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parwWxw0.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parwWxw0.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x020.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"17\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_17\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/paroNaAJ.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/paroNaAJ.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/paroNaAJ.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/paroNaAJ.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/paroNaAJ.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x003.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"18\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_18\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parchOGP.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parchOGP.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parchOGP.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parchOGP.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parchOGP.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x020.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"20\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_20\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parVhSi8.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parVhSi8.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parVhSi8.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parVhSi8.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parVhSi8.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x003.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"21\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_21\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/pareLiHn.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/pareLiHn.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/pareLiHn.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/pareLiHn.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/pareLiHn.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x003.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"23\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_23\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parse3wL.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parse3wL.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parse3wL.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parse3wL.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parse3wL.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x003.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"6\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_6\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parQh5eJ.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parQh5eJ.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parQh5eJ.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parQh5eJ.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parQh5eJ.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x003.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"27\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_27\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parnuokL.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parnuokL.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parnuokL.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parnuokL.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parnuokL.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x020.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"25\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_25\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parmXJ5N.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parmXJ5N.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parmXJ5N.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parmXJ5N.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parmXJ5N.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x020.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"26\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_26\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parXM76W.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parXM76W.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parXM76W.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parXM76W.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parXM76W.chr; >> cat - ) | (/afs/enea.it/software/bin/blaunch.sh >> cresco3x020.portici.enea.it exec perl -e >> \\\$ENV\\\{\\\"PARALLEL_PID\\\"\\\}=\\\"22663\\\"\\\;\\\$ENV\\\{\\\"PARALLEL_SEQ\\\"\\\}=\\\"24\\\"\\\;\\\$bashfunc\\\ >> =\\\ \\\"\\\"\\\;@ARGV=\\\"blastp\\\ -evalue\\\ 1e-05\\\ -outfmt\\\ 6\\\ >> -db\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000\\\ >> -query\\\ -\\\ -out\\\ >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_24\\\"\\\;\\\$SIG\\\{CHLD\\\}=sub\\\{\\\$done=1\\\;\\\}\\\;\\\$pid=fork\\\;unless\\\(\\\$pid\\\)\\\{setpgrp\\\;exec\\\$ENV\\\{SHELL\\\},\\\"-c\\\",\\\(\\\$bashfunc.\\\"@ARGV\\\"\\\)\\\;die\\\"exec:\\\$\\\!\\\\n\\\"\\\;\\\}do\\\{\\\$s=\\\$s\\\<1\\\?0.001+\\\$s\\\*1.03:\\\$s\\\;select\\\(undef,undef,undef,\\\$s\\\)\\\;\\\}until\\\(\\\$done\\\|\\\|getppid==1\\\)\\\;kill\\\(SIGHUP,-\\\$\\\{pid\\\}\\\)unless\\\$done\\\;wait\\\;exit\\\(\\\$\\\?\\\&127\\\?128+\\\(\\\$\\\?\\\&127\\\):1+\\\$\\\?\\\>\\\>8\\\);); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/pargNN8b.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/pargNN8b.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/pargNN8b.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/pargNN8b.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/pargNN8b.chr; >> cat - ) | (blastp -evalue 1e-05 -outfmt 6 -db >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000 >> -query - -out >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_10); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parf3mob.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parf3mob.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parf3mob.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parf3mob.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parf3mob.chr; >> cat - ) | (blastp -evalue 1e-05 -outfmt 6 -db >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000 >> -query - -out >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_7); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parGTSb6.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parGTSb6.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parGTSb6.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parGTSb6.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parGTSb6.chr; >> cat - ) | (blastp -evalue 1e-05 -outfmt 6 -db >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000 >> -query - -out >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_16); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parxwGS2.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parxwGS2.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parxwGS2.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parxwGS2.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parxwGS2.chr; >> cat - ) | (blastp -evalue 1e-05 -outfmt 6 -db >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000 >> -query - -out >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_4); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parCrFM_.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parCrFM_.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parCrFM_.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parCrFM_.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parCrFM_.chr; >> cat - ) | (blastp -evalue 1e-05 -outfmt 6 -db >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000 >> -query - -out >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_1); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par7fOlu.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par7fOlu.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par7fOlu.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par7fOlu.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/par7fOlu.chr; >> cat - ) | (blastp -evalue 1e-05 -outfmt 6 -db >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000 >> -query - -out >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_19); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parKlqXO.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parKlqXO.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parKlqXO.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parKlqXO.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parKlqXO.chr; >> cat - ) | (blastp -evalue 1e-05 -outfmt 6 -db >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000 >> -query - -out >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_22); >> sh -c 'dd bs=1 count=1 >> of=/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parsuHqk.chr >> 2>/dev/null'; test ! -s >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parsuHqk.chr" >> && rm -f >> "/gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parsuHqk.chr" >> && exec true; (cat >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parsuHqk.chr; >> rm >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/tmp/parsuHqk.chr; >> cat - ) | (blastp -evalue 1e-05 -outfmt 6 -db >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/goodProteins_first_0010000 >> -query - -out >> /gporq1_1M/usr/aprea/bio/solanum_melongena/analysis/orthomcl_00/resultd_13); >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> Apr 16 17:47:26 2015 22805 3 7.03 lsb_launch(): Failed while executing >> tasks. >> Apr 16 17:47:27 2015 22885 3 7.03 lsb_launch(): Connection refused by >> server. >> Apr 16 17:47:27 2015 22938 3 7.03 lsb_launch(): Connection refused by >> server. >> Apr 16 17:47:27 2015 22939 3 7.03 lsb_launch(): Connection refused by >> server. >> Apr 16 17:47:27 2015 22924 3 7.03 lsb_launch(): Connection refused by >> server. >> Apr 16 17:47:26 2015 22802 3 7.03 lsb_launch(): Failed while executing >> tasks. >> Apr 16 17:47:27 2015 22928 3 7.03 lsb_launch(): Connection refused by >> server. >> Apr 16 17:47:27 2015 22946 3 7.03 lsb_launch(): Connection refused by >> server. >> Apr 16 17:47:27 2015 22950 3 7.03 lsb_launch(): Connection refused by >> server. >> Apr 16 17:47:27 2015 22923 3 7.03 lsb_launch(): Connection refused by >> server. >> Apr 16 17:47:27 2015 22951 3 7.03 lsb_launch(): Connection refused by >> server. >> Apr 16 17:47:27 2015 22952 3 7.03 lsb_launch(): Connection refused by >> server. >> Apr 16 17:47:27 2015 22915 3 7.03 lsb_launch(): Connection refused by >> server. >> Apr 16 17:47:27 2015 23022 3 7.03 lsb_launch(): Connection refused by >> server. >> Apr 16 17:47:27 2015 22787 3 7.03 lsb_launch(): Failed while executing >> tasks. >> Apr 16 17:47:27 2015 23046 3 7.03 lsb_launch(): Connection refused by >> server. >> Apr 16 17:47:27 2015 23054 3 7.03 lsb_launch(): Connection refused by >> server. >> Apr 16 17:47:27 2015 23058 3 7.03 lsb_launch(): Connection refused by >> server. >> Apr 16 17:47:27 2015 23053 3 7.03 lsb_launch(): Connection refused by >> server. >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> the server file is >> >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> /afs/enea.it/software/bin/blaunch.sh cresco3x003.portici.enea.it >> /afs/enea.it/software/bin/blaunch.sh cresco3x003.portici.enea.it >> /afs/enea.it/software/bin/blaunch.sh cresco3x003.portici.enea.it >> /afs/enea.it/software/bin/blaunch.sh cresco3x003.portici.enea.it >> /afs/enea.it/software/bin/blaunch.sh cresco3x003.portici.enea.it >> /afs/enea.it/software/bin/blaunch.sh cresco3x020.portici.enea.it >> /afs/enea.it/software/bin/blaunch.sh cresco3x020.portici.enea.it >> /afs/enea.it/software/bin/blaunch.sh cresco3x020.portici.enea.it >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> -------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> And the master node is cresco3x003 >> >> I don't understand the output from -vv options very well but, as you can >> see (I hope) the last 8 lines from stdout (with indices >> 1,4,7,10,13,16,19,22) are different and they correspond to the 8 output >> file I finally retrieve. I would have expected the same lines at least for >> the first 5 indices (1,2,3,4,5) since PARALLEL eventually could have >> recognized it was on the local host but that's not the case and I find that >> strange.... >> >> Does anybody have an idea of what's going on? >> >> Ciao, >> >> Giuseppe >> >> PS I remind I am using version 20150122 >> >> >> >> >> On Thu, Apr 16, 2015 at 3:49 PM, George Marselis <geo...@marsel.is> >> wrote: >> >>> You could do that, and it might work, if you are interested in using the >>> LSF API >>> >>> otherwise, use a batch script and blaunch < batchscript.sh , instead. >>> >>> Ciao, >>> >>> George >>> >>> On Thu, Apr 16, 2015 at 9:24 AM, Giuseppe Aprea < >>> giuseppe.ap...@gmail.com> wrote: >>> >>>> Dear George, >>>> >>>> I was not sure you were talking to me because I am submitting 1 job >>>> only. Then I am using blaunch as a spawn agent instead of shh because this >>>> is the way our cluster works. Mpi jobs with several hundreds slots also use >>>> it (orte_rsh_agent MCA parameter). >>>> >>>> What do you think if I replace >>>> >>>> --recstart '>' -N 1 --pipe >>>> >>>> with >>>> >>>> --recstart '>' -block 100k --pipe >>>> >>>> ? >>>> >>>> I think I could reduce load on lsb_launch() using a larger data chunk, >>>> couldn't I? >>>> >>>> cheers, >>>> >>>> g >>>> >>>> >>>> >>>> On Wed, Apr 15, 2015 at 10:32 PM, George Marselis <geo...@marsel.is> >>>> wrote: >>>> >>>>> > You could use parallel to submit jobs, but its a very bad idea, due >>>>> to the limitations of the software. >>>>> >>>>> >>>>> and by that, I mean the limitations of the LSF software. >>>>> >>>>> Parallel rocks. Ole rocks. >>>>> >>>>> Next Parallel Release should be named "GNU Terry Pratchett" >>>>> >>>>> > Let me know which option is better for you. >>>>> > As with regard to Martin, he should not use parallel for >>>>> >>>>> ^-- this is your brain on Perl. >>>>> >>>>> Best Regards, >>>>> >>>>> George >>>>> >>>>> >>>>> On Wed, Apr 15, 2015 at 11:27 PM, George Marselis <geo...@marsel.is> >>>>> wrote: >>>>> >>>>>> Giuseppe, I was referring to both of you. My apologies I was not >>>>>> clear, I had my head stuck in Perl while writing the first email. >>>>>> >>>>>> My suggestion to both of you is that you should not use parallel for >>>>>> your respective topics. >>>>>> >>>>>> Giuseppe, >>>>>> >>>>>> You should use an extra script. Your problem is that you are timing >>>>>> out while trying to submit all those jobs. The timeout happens because of >>>>>> the number of jobs you are submitting: LSF cannot write the job >>>>>> descriptions fast enough to disk, times out because the action is not >>>>>> completed and then stays in that state >>>>>> >>>>>> ---------------- >>>>>> Martin, >>>>>> >>>>>> You could use parallel to submit jobs, but its a very bad idea, due >>>>>> to the limitations of the software. Use batch scripts and job arrays when >>>>>> possible. >>>>>> >>>>>> ---------------- >>>>>> >>>>>> So, as per my suggestion, I think our discussion is offtopic for this >>>>>> list. We could continue here, if Ole and the list puts up with us, but I >>>>>> think we should take this on a personal email or switch this to the >>>>>> Debian >>>>>> Medical email list https://en.wikipedia.org/wiki/Debian-Med . >>>>>> >>>>>> Let me know which option is better for you. >>>>>> >>>>>> As with regard to Martin, he should not use parallel for >>>>>> >>>>>> >>>>>> Ciao, >>>>>> >>>>>> George >>>>>> >>>>>> On Wed, Apr 15, 2015 at 10:50 PM, Giuseppe Aprea < >>>>>> giuseppe.ap...@gmail.com> wrote: >>>>>> >>>>>>> Hi George! >>>>>>> >>>>>>> I am not sure who you are talking with. Martin or me? I remind the >>>>>>> original topic is about using blast under parallel with LSF. >>>>>>> Martin's problem sounds like something offtopic. >>>>>>> >>>>>>> You have both sysadmin and bioinformatics experience so I would >>>>>>> really appreciate your help! >>>>>>> >>>>>>> I am working on a cluster so I must use LSF to get slots and I would >>>>>>> prefer using parallel also since it splits input automatically with >>>>>>> --recstart (which is quite nice:D otherwise I have to use another script >>>>>>> for that). I see I could do better with chunksize (I have 1 record at >>>>>>> time >>>>>>> in my example) but that's a secondary problem now. First I have the >>>>>>> "lsb_launch(): Failed while waiting for tasks to finish." issue to >>>>>>> solve. >>>>>>> >>>>>>> cheers, >>>>>>> >>>>>>> g >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Wed, Apr 15, 2015 at 7:44 PM, George Marselis <geo...@marsel.is> >>>>>>> wrote: >>>>>>> >>>>>>>> By the way, LSF and GNU parallel do almost the same thing. So using >>>>>>>> one of the two, defeats the purpose of using the other. >>>>>>>> >>>>>>>> In the same way, you could have used LSF to submit your jobs to LSF: >>>>>>>> >>>>>>>> bsub < script.sh >>>>>>>> >>>>>>>> where script.sh was >>>>>>>> >>>>>>>> bsub -J amoeba -q smalljobs qfasta file1 >>>>>>>> bsub -J amoeba -q smalljobs qfasta file2 >>>>>>>> ... >>>>>>>> bsub -J amoeba -q smalljobs qfasta file2000 >>>>>>>> >>>>>>>> On Wed, Apr 15, 2015 at 8:39 PM, George Marselis <geo...@marsel.is> >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi. LSF/Openlava sysadmin in bioinformatics and parallel user here. >>>>>>>>> >>>>>>>>> I have seen this a couple more times: You are trying to use GNU >>>>>>>>> parallel to submit the jobs to all nodes. >>>>>>>>> >>>>>>>>> THat's now the way to do things: You should not submit jobs on >>>>>>>>> *all* your nodes. Please don't do that, as bsub was not designed to >>>>>>>>> read >>>>>>>>> large chunks of jobs. bsub writes the jobs to your home directory, so >>>>>>>>> if >>>>>>>>> your storage is not designed for a lot of writes, you are going to >>>>>>>>> blow the >>>>>>>>> cluster out of the water. >>>>>>>>> >>>>>>>>> What you want to do is look up either: >>>>>>>>> >>>>>>>>> 1. bsub scripts >>>>>>>>> https://rc.fas.harvard.edu/resources/documentation/legacy-lsf/lsf-submit-an-lsf-job/ >>>>>>>>> >>>>>>>>> or >>>>>>>>> >>>>>>>>> 2. job arrays >>>>>>>>> https://rc.fas.harvard.edu/resources/documentation/legacy-lsf/lsf-submitting-lots-of-short-jobs-job-arrays/ >>>>>>>>> >>>>>>>>> Both bsub scripts and job arrays are useful to you: bsub scripts >>>>>>>>> can be submitted as part of a pipeline: you can program the output of >>>>>>>>> the >>>>>>>>> bsub script from your pipeline and then submit it to bsub. So, >>>>>>>>> instead of >>>>>>>>> submitting your job 2000 times as in >>>>>>>>> >>>>>>>>> bsub job0 >>>>>>>>> bsub job1 >>>>>>>>> >>>>>>>>> .... >>>>>>>>> >>>>>>>>> bsub job1999 >>>>>>>>> >>>>>>>>> you just submit "bsub < scriptname" which contains 2000 lines >>>>>>>>> which describe your jobs and you are done. The rest is done by >>>>>>>>> bsub/LSF >>>>>>>>> >>>>>>>>> >>>>>>>>> Now, if your jobs are similar in a way that you just increment >>>>>>>>> counter (as in most bioinformatics jobs), use arrays. >>>>>>>>> >>>>>>>>> bsub -J JOBNAME[0-1999], where JOBNAME is a string you would like >>>>>>>>> to name your job as, eg "fasta files alignment" >>>>>>>>> >>>>>>>>> >>>>>>>>> These techniques are useful because you can submit all 2000 jobs >>>>>>>>> in less than a second, you can do it from a single node and you will >>>>>>>>> not >>>>>>>>> have to deal with a grumpy sysadmin or grumpy colleagues who cannot >>>>>>>>> use the >>>>>>>>> cluster. Just make sure you use the appropriate queue. >>>>>>>>> >>>>>>>>> Let me know if you have any questions. >>>>>>>>> >>>>>>>>> Best Regards, >>>>>>>>> >>>>>>>>> George Marselis >>>>>>>>> >>>>>>>>> On Wed, Apr 15, 2015 at 6:48 PM, Martin d'Anjou < >>>>>>>>> martin.danjo...@gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> Thanks for clarifying. I want to use GNU Parallel to bsub jobs. >>>>>>>>>> This way I can use GNU Parallel to throttle the number of jobs that >>>>>>>>>> are >>>>>>>>>> submitted to LSF, and it is easier than writing a loop. >>>>>>>>>> >>>>>>>>>> parallel -j 100 my_script [bsub options] ::: {1..2000} >>>>>>>>>> >>>>>>>>>> my_script (pseudo-code): >>>>>>>>>> #!/bin/bash >>>>>>>>>> ... >>>>>>>>>> bsub [bsub options] command ... >>>>>>>>>> post-process data >>>>>>>>>> >>>>>>>>>> This way I can submit jobs, say 100 at a time. When I submit all >>>>>>>>>> 2000 jobs, it gets problematic and I start hitting limits with file >>>>>>>>>> descriptors, etc. >>>>>>>>>> >>>>>>>>>> Thanks for sharing, >>>>>>>>>> Martin >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 15-04-15 11:35 AM, Giuseppe Aprea wrote: >>>>>>>>>> >>>>>>>>>> Hi Martin, >>>>>>>>>> >>>>>>>>>> I am not sure I understand. As far as I can see, things work >>>>>>>>>> exactly the opposite way: you have an LSF script which launches GNU >>>>>>>>>> Parallel on some hosts provided by LSF. Something like: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ------------------------------------------------------------------------------- >>>>>>>>>> >>>>>>>>>> ------------------------------------------------------------------------------- >>>>>>>>>> #!/bin/bash >>>>>>>>>> >>>>>>>>>> #BSUB -J gnuParallel_blast_test # Name of the job. >>>>>>>>>> #BSUB -o %J.out # Appends std output >>>>>>>>>> to file %J.out. (%J is the Job ID) >>>>>>>>>> #BSUB -e %J.err # Appends std error >>>>>>>>>> to file %J.err. >>>>>>>>>> #BSUB -q large # Queue name. >>>>>>>>>> #BSUB -n 30 # Number of CPUs. >>>>>>>>>> >>>>>>>>>> module load 4.8.3/ncbi/12.0.0 >>>>>>>>>> module load 4.8.3/parallel/20150122 >>>>>>>>>> >>>>>>>>>> SLOTS=`cat ${LSB_DJOB_HOSTFILE} |wc -l` >>>>>>>>>> >>>>>>>>>> SERVER="" >>>>>>>>>> >>>>>>>>>> for i in `cat ${LSB_DJOB_HOSTFILE}| sort` >>>>>>>>>> do >>>>>>>>>> echo "/afs/enea.it/software/bin/blaunch.sh ${i}" >> servers >>>>>>>>>> done >>>>>>>>>> >>>>>>>>>> cat absolute_path_to_sequences.fasta | parallel --no-notice -vv >>>>>>>>>> -j ${SLOTS} --slf servers --plain --recstart '>' -N 1 --pipe blastp >>>>>>>>>> -evalue >>>>>>>>>> 1e-05 -outfmt 6 -db absolute_path_to_db_file -query - -out >>>>>>>>>> absolute_path_to_result_file_{%} >>>>>>>>>> >>>>>>>>>> ------------------------------------------------------------------------------- >>>>>>>>>> >>>>>>>>>> ------------------------------------------------------------------------------- >>>>>>>>>> >>>>>>>>>> LSF is the one which gives you the execution hosts so if you >>>>>>>>>> are launching bsub from GNU parallel how do you know how to set the >>>>>>>>>> --slf >>>>>>>>>> option? >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> g >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Wed, Apr 15, 2015 at 4:24 PM, Martin d'Anjou < >>>>>>>>>> martin.danjo...@gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> On 15-04-15 09:34 AM, Giuseppe Aprea wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi all, >>>>>>>>>>>> >>>>>>>>>>>> I would like to ask you, please, some help in using parallel >>>>>>>>>>>> with blast alignment software. >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> I am trying to use GNU parallel v. 20150122 with blast for a >>>>>>>>>>>> very large sequences alignment. I am using Parallel on a cluster >>>>>>>>>>>> which uses >>>>>>>>>>>> LSF as queue system. >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Hello Giuseppe, >>>>>>>>>>> >>>>>>>>>>> I am an avid LSF user, and I want to use GNU Parallel to >>>>>>>>>>> dispatch jobs to LSF. Could you please explain a little bit to me >>>>>>>>>>> how GNU >>>>>>>>>>> Parallel works with LSF? I do not see it in the on-line tutorials. >>>>>>>>>>> For >>>>>>>>>>> example, I would like to understand how to pass "bsub" options like >>>>>>>>>>> -oo, -q >>>>>>>>>>> queue_name, etc. to LSF from GNU Parallel. >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> Martin >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >