LSF DRMAA/FedStage config-make errors
Hello all, I am trying to get a Galaxy server configured to submit jobs to an LSF cluster running version 7 update 2, generally CentOS/Redhat 5 systems. I have the Galaxy host as a client in LSF, but when I tried to configure/make/install the FedStage drmaa code, it errors out in the make stage (see stdout below). Don't know what to fix, if it's possible. If anyone has experience configuring/troubleshooting this code to get Galaxy conversant with LSF, I'd appreciate any feedback. Thanks! Regards, Doug _________ util.c: In function 'lsfdrmaa_map_lsberrno': util.c:730: error: 'LSBE_ADRSV_ID_UNIQUE' undeclared (first use in this function) util.c:730: error: (Each undeclared identifier is reported only once util.c:730: error: for each function it appears in.) util.c:731: error: 'LSBE_BAD_RSVNAME' undeclared (first use in this function) util.c:732: error: 'LSBE_BAD_CHKPNTDIR' undeclared (first use in this function) util.c:734: error: 'LSBE_JOB_REQUEUE_BADEXCLUDE' undeclared (first use in this function) util.c:737: error: 'LSBE_ADVRSV_ACTIVESTART' undeclared (first use in this function) util.c:739: error: 'LSBE_ADRSV_ID_USED' undeclared (first use in this function) util.c:740: error: 'LSBE_ADRSV_PREVDISABLED' undeclared (first use in this function) util.c:742: error: 'LSBE_ADRSV_DISABLECURR' undeclared (first use in this function) util.c:744: error: 'LSBE_ADRSV_NOT_RSV_HOST' undeclared (first use in this function) util.c:749: error: 'LSBE_ADRSV_MOD_REMOTE' undeclared (first use in this function) util.c:751: error: 'LSBE_JOB_RUSAGE_EXCEED_LIMIT' undeclared (first use in this function) util.c:752: error: 'LSBE_APP_RUSAGE_EXCEED_LIMIT' undeclared (first use in this function) util.c:755: error: 'LSBE_ADRSV_DISABLE_DATE' undeclared (first use in this function) util.c:759: error: 'LSBE_ADRSV_DETACH_MIX' undeclared (first use in this function) util.c:761: error: 'LSBE_ADRSV_DETACH_ACTIVE' undeclared (first use in this function) util.c:765: error: 'LSBE_MISSING_START_END_TIME' undeclared (first use in this function) make[3]: *** [libdrmaa_la-util.lo] Error 1 make[3]: Leaving directory `/root/installers/lsf_drmaa-1.0.4/lsf_drmaa' make[2]: *** [all] Error 2 make[2]: Leaving directory `/root/installers/lsf_drmaa-1.0.4/lsf_drmaa' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/root/installers/lsf_drmaa-1.0.4' (Same output with version 1.0.3.) This communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html
On Aug 29, 2012, at 12:41 PM, Douglas W Cloud wrote:
Hello all, I am trying to get a Galaxy server configured to submit jobs to an LSF cluster running version 7 update 2, generally CentOS/Redhat 5 systems. I have the Galaxy host as a client in LSF, but when I tried to configure/make/install the FedStage drmaa code, it errors out in the make stage (see stdout below). Don't know what to fix, if it's possible.
If anyone has experience configuring/troubleshooting this code to get Galaxy conversant with LSF, I'd appreciate any feedback. Thanks!
Regards, Doug _________
util.c: In function 'lsfdrmaa_map_lsberrno': util.c:730: error: 'LSBE_ADRSV_ID_UNIQUE' undeclared (first use in this function) util.c:730: error: (Each undeclared identifier is reported only once util.c:730: error: for each function it appears in.) util.c:731: error: 'LSBE_BAD_RSVNAME' undeclared (first use in this function) util.c:732: error: 'LSBE_BAD_CHKPNTDIR' undeclared (first use in this function) util.c:734: error: 'LSBE_JOB_REQUEUE_BADEXCLUDE' undeclared (first use in this function) util.c:737: error: 'LSBE_ADVRSV_ACTIVESTART' undeclared (first use in this function) util.c:739: error: 'LSBE_ADRSV_ID_USED' undeclared (first use in this function) util.c:740: error: 'LSBE_ADRSV_PREVDISABLED' undeclared (first use in this function) util.c:742: error: 'LSBE_ADRSV_DISABLECURR' undeclared (first use in this function) util.c:744: error: 'LSBE_ADRSV_NOT_RSV_HOST' undeclared (first use in this function) util.c:749: error: 'LSBE_ADRSV_MOD_REMOTE' undeclared (first use in this function) util.c:751: error: 'LSBE_JOB_RUSAGE_EXCEED_LIMIT' undeclared (first use in this function) util.c:752: error: 'LSBE_APP_RUSAGE_EXCEED_LIMIT' undeclared (first use in this function) util.c:755: error: 'LSBE_ADRSV_DISABLE_DATE' undeclared (first use in this function) util.c:759: error: 'LSBE_ADRSV_DETACH_MIX' undeclared (first use in this function) util.c:761: error: 'LSBE_ADRSV_DETACH_ACTIVE' undeclared (first use in this function) util.c:765: error: 'LSBE_MISSING_START_END_TIME' undeclared (first use in this function) make[3]: *** [libdrmaa_la-util.lo] Error 1 make[3]: Leaving directory `/root/installers/lsf_drmaa-1.0.4/lsf_drmaa' make[2]: *** [all] Error 2 make[2]: Leaving directory `/root/installers/lsf_drmaa-1.0.4/lsf_drmaa' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/root/installers/lsf_drmaa-1.0.4'
Hi Doug, It looks like you probably need to include whatever header file from LSF contains these declarations. I don't have an LSF installation so I don't know what file that is, but it would presumably be with the other LSF includes. You may also want to contact the lsf-drmaa developers or Platform for more specific support. --nate
(Same output with version 1.0.3.)
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participants (2)
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Douglas W Cloud -
Nate Coraor