Running Galaxy Jobs On Pbs Pro Cluster

Question: Running Galaxy Jobs On Pbs Pro Cluster

8.1 years ago by

Hello, I'm having some troubles installing pbs_drmaa-1.0.2.tar.gz (http://sourceforge.net/projects/pbspro-drmaa/) with pbs pro (./configure fails). Have anyone already succeeded in installing galaxy to run jobs on pbs pro ? Thanks, Laure -- Laure QUINTRIC Ifremer - IDM/RIC Technopôle Brest-Iroise 29280 Plouzané Tel: 02 98 22 49 11 - Fax : 02 98 22 46 47 E-mail : Laure.Quintric@ifremer.fr

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modified 8.1 years ago by Nate Coraor ♦ 3.2k • written 8.1 years ago by Laure QUINTRIC • 20

8.1 years ago by

Nate Coraor ♦ 3.2k

United States

Nate Coraor ♦ 3.2k wrote:

Hi Laure, I have not used PBS Pro recently, nor do I have access to it. However, we may be able to help if you paste the error message you're receiving from ./configure. Thanks, --nate

ADD COMMENT • link written 8.1 years ago by Nate Coraor ♦ 3.2k

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

ADD REPLY • link written 8.1 years ago by Laure QUINTRIC • 20

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