Re: [galaxy-dev] running galaxy jobs on pbs pro cluster
Hi Laure, I just noticed this was posted on our user list, while it's probably more appropriate for the dev list. So I've moved the conversation there. Please consider subscribing, if you haven't already. The failure to find PBS is further up in the log, since this is a failure to find the TORQUE library, and you're trying to build against PBS Pro. However as of yesterday there's a new version (1.0.3) out that may solve this problem? You should probably try that and see if it works. --nate Laure QUINTRIC wrote:
Hi Nate,
For installing pbs_drmaa package we launch fisrt: ./configure --prefix=/appli/drmaa/1.0.2 --with-pbs=/appli/pbs/sles11/exec/10.4.0.101257
--with-pbs path we set is pbs pro root directory.
In config.log file, the error log is the following :
configure:12206: gcc -o conftest -pedantic -ansi -g -O2 -pthread -D_REENTRANT -D_THREAD_SAFE -DNDEBUG -D_GNU_SOURCE -I/appli/pbs/sles11/exec/10.4.0.101 257/include -L/appli/pbs/sles11/exec/10.4.0.101257/lib -Wl,-R/appli/pbs/sles11/exec/10.4.0.101257/lib conftest.c -ltorque -pthread >&5 /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: cannot find -ltorque collect2: ld returned 1 exit status configure:12213: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "FedStage DRMAA for PBS Pro" | #define PACKAGE_TARNAME "pbs_drmaa" | #define PACKAGE_VERSION "1.0.2" | #define PACKAGE_STRING "FedStage DRMAA for PBS Pro 1.0.2" | #define PACKAGE_BUGREPORT "mamonski@man.poznan.pl" | #define PACKAGE "pbs_drmaa" | #define VERSION "1.0.2" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | | /* Override any GCC internal prototype to avoid an error. | Use char because int might match the return type of a GCC | builtin and then its argument prototype would still apply. */ | #ifdef __cplusplus | extern "C" | #endif | char pbse_to_txt (); | int | main () | { | return pbse_to_txt (); | ; | return 0; | } configure:12234: result: no configure:12413: error: PBS libraries/headers not found; add --with-pbs to set PBS installation root.
Headers and libraries are not found although there are located in the path we set in --with-pbs option :
service>108% ls /appli/pbs/sles11/exec/10.4.0.101257 bin etc include lib man python sbin tcltk unsupported
service>109% ls /appli/pbs/sles11/exec/10.4.0.101257/include/ pbs_error.h pbs_ifl.h rm.h tm.h tm_.h
service>110% ls /appli/pbs/sles11/exec/10.4.0.101257/lib MPI ical init.d libattr.a liblog.a libnet.a libpbs.a libsite.a pbs_sched.a pm python xpbs xpbsmon
it seems we are not the only one having this issue with pbs pro. Do you have any idea ?
Thanks, Laure
Hi Laure this is the configure that worked for me with 1.0.3 (1.0.2 does not work with pbspro 10): ./configure --with-pbs=/opt/pbs/default/ --with-drmaa --prefix=$HOME/pbs_drmaa (/opt/pbs/default has the include/ & lib/ dirs) However, I cannot get the drmaa-python to work with 1.0.3, following the tutorial. The first 2 examples work, getting a session, but the third; submitting a job, does not work for me. http://code.google.com/p/drmaa-python/wiki/Tutorial I havent tried with galaxy yet since the basic drmaa-python interface seems problematic. Cheers M -- Dr Michael Pheasant Software Engineer Queensland Facility for Advanced Bioinformatics Level 5, QBP University of Queensland, QLD 4072 T: +61 (0)7 3346 2070 F: +61 (0)7 3346 2101 www.qfab.org On Thu, Oct 21, 2010 at 12:04 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Hi Laure,
I just noticed this was posted on our user list, while it's probably more appropriate for the dev list. So I've moved the conversation there. Please consider subscribing, if you haven't already.
The failure to find PBS is further up in the log, since this is a failure to find the TORQUE library, and you're trying to build against PBS Pro.
However as of yesterday there's a new version (1.0.3) out that may solve this problem? You should probably try that and see if it works.
--nate
Laure QUINTRIC wrote:
Hi Nate,
For installing pbs_drmaa package we launch fisrt: ./configure --prefix=/appli/drmaa/1.0.2 --with-pbs=/appli/pbs/sles11/exec/10.4.0.101257
--with-pbs path we set is pbs pro root directory.
In config.log file, the error log is the following :
configure:12206: gcc -o conftest -pedantic -ansi -g -O2 -pthread -D_REENTRANT -D_THREAD_SAFE -DNDEBUG -D_GNU_SOURCE -I/appli/pbs/sles11/exec/10.4.0.101 257/include -L/appli/pbs/sles11/exec/10.4.0.101257/lib -Wl,-R/appli/pbs/sles11/exec/10.4.0.101257/lib conftest.c -ltorque -pthread >&5 /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: cannot find -ltorque collect2: ld returned 1 exit status configure:12213: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "FedStage DRMAA for PBS Pro" | #define PACKAGE_TARNAME "pbs_drmaa" | #define PACKAGE_VERSION "1.0.2" | #define PACKAGE_STRING "FedStage DRMAA for PBS Pro 1.0.2" | #define PACKAGE_BUGREPORT "mamonski@man.poznan.pl" | #define PACKAGE "pbs_drmaa" | #define VERSION "1.0.2" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | | /* Override any GCC internal prototype to avoid an error. | Use char because int might match the return type of a GCC | builtin and then its argument prototype would still apply. */ | #ifdef __cplusplus | extern "C" | #endif | char pbse_to_txt (); | int | main () | { | return pbse_to_txt (); | ; | return 0; | } configure:12234: result: no configure:12413: error: PBS libraries/headers not found; add --with-pbs to set PBS installation root.
Headers and libraries are not found although there are located in the path we set in --with-pbs option :
service>108% ls /appli/pbs/sles11/exec/10.4.0.101257 bin etc include lib man python sbin tcltk unsupported
service>109% ls /appli/pbs/sles11/exec/10.4.0.101257/include/ pbs_error.h pbs_ifl.h rm.h tm.h tm_.h
service>110% ls /appli/pbs/sles11/exec/10.4.0.101257/lib MPI ical init.d libattr.a liblog.a libnet.a libpbs.a libsite.a pbs_sched.a pm python xpbs xpbsmon
it seems we are not the only one having this issue with pbs pro. Do you have any idea ?
Thanks, Laure
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
*) Anyone have drmaa-python (or Galaxy, for that matter) working with PBS Pro 10? I logged a problem with drmaa-python, I cant get the example programs to successfully submit a job: http://code.google.com/p/drmaa-python/issues/detail?id=24 -- Dr Michael Pheasant Software Engineer Queensland Facility for Advanced Bioinformatics Level 5, QBP University of Queensland, QLD 4072 T: +61 (0)7 3346 2070 F: +61 (0)7 3346 2101 www.qfab.org On Thu, Oct 21, 2010 at 12:04 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Hi Laure,
I just noticed this was posted on our user list, while it's probably more appropriate for the dev list. So I've moved the conversation there. Please consider subscribing, if you haven't already.
The failure to find PBS is further up in the log, since this is a failure to find the TORQUE library, and you're trying to build against PBS Pro.
However as of yesterday there's a new version (1.0.3) out that may solve this problem? You should probably try that and see if it works.
--nate
Laure QUINTRIC wrote:
Hi Nate,
For installing pbs_drmaa package we launch fisrt: ./configure --prefix=/appli/drmaa/1.0.2 --with-pbs=/appli/pbs/sles11/exec/10.4.0.101257
--with-pbs path we set is pbs pro root directory.
In config.log file, the error log is the following :
configure:12206: gcc -o conftest -pedantic -ansi -g -O2 -pthread -D_REENTRANT -D_THREAD_SAFE -DNDEBUG -D_GNU_SOURCE -I/appli/pbs/sles11/exec/10.4.0.101 257/include -L/appli/pbs/sles11/exec/10.4.0.101257/lib -Wl,-R/appli/pbs/sles11/exec/10.4.0.101257/lib conftest.c -ltorque -pthread >&5 /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: cannot find -ltorque collect2: ld returned 1 exit status configure:12213: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "FedStage DRMAA for PBS Pro" | #define PACKAGE_TARNAME "pbs_drmaa" | #define PACKAGE_VERSION "1.0.2" | #define PACKAGE_STRING "FedStage DRMAA for PBS Pro 1.0.2" | #define PACKAGE_BUGREPORT "mamonski@man.poznan.pl" | #define PACKAGE "pbs_drmaa" | #define VERSION "1.0.2" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | | /* Override any GCC internal prototype to avoid an error. | Use char because int might match the return type of a GCC | builtin and then its argument prototype would still apply. */ | #ifdef __cplusplus | extern "C" | #endif | char pbse_to_txt (); | int | main () | { | return pbse_to_txt (); | ; | return 0; | } configure:12234: result: no configure:12413: error: PBS libraries/headers not found; add --with-pbs to set PBS installation root.
Headers and libraries are not found although there are located in the path we set in --with-pbs option :
service>108% ls /appli/pbs/sles11/exec/10.4.0.101257 bin etc include lib man python sbin tcltk unsupported
service>109% ls /appli/pbs/sles11/exec/10.4.0.101257/include/ pbs_error.h pbs_ifl.h rm.h tm.h tm_.h
service>110% ls /appli/pbs/sles11/exec/10.4.0.101257/lib MPI ical init.d libattr.a liblog.a libnet.a libpbs.a libsite.a pbs_sched.a pm python xpbs xpbsmon
it seems we are not the only one having this issue with pbs pro. Do you have any idea ?
Thanks, Laure
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participants (2)
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Michael Pheasant -
Nate Coraor