[Frost] Computer/Environment issues with g9b TOF Calibration
Arthur Sabintsev
arthur at jlab.org
Tue Jun 22 15:45:21 EDT 2010
Good Afternoon,
I'm having a few issues doing the g9b TOF calibration. It's not due to the
data, but rather, getting certain packages from the CLAS repository (CVS,
not SVN) to either compile or run.
In a nutshell, GWU currently doesn't have a suitable workstation onsite, so
I am connecting to the 32- and 64-bit farms via ssh/vnc from my laptop. I'm
physically onsite though.
I've tried to get these packages up and running on my personal account
(/home/arthur/clas) and the existing packages on the clasg9 account
(/home/clasg9):
To my knowledge, the software packages I need for the calibration are (not
sure, because documentation is a bit limited):
1. cms (located in /packages/)
2. ClasTool (located in /packages/)
3. TPhotTiming (located in /packages/utilities/sc_calib)
4. gamecock (located in /packages/utilities/sc_calib)
5. veff (located in /packages/utilities/sc_calib)
6. time_walk (located in /packages/utilities/sc_calib)
So far, only ClasTool and Gamecock have been successfully compiled, but only
on a 32-bit farm and on my account.
Gamecock gives some odd errors when I try running it (through VNC) on a
32-bit machine.
For the other packages I mentioned, the errors that occur are either:
1. Compiler related,
2. During compilation, a directory ~/home/arthur/clas/slib is not found.
3. or Links/Flags to *.Linux64RH5.mk are not found in packages/cms
directory.
I'm not sure if I can use a different gcc compiler on any of these machines
(and if I can, which versions should I use)?
Also, how do I create the missing link/flag files for 64-bith RHEL5
machines?
the first error causes problems with 32-bit machines. The latter two issues
are the root of all compilation issues for 64-bit machines.
I've attached three small text documents to this email. The first two
contain errors that I get while compiling on the two different types of
farms (and minor commentary on my understanding of the errors), and the
third is my environment file (tcsh).
1. errors32.txt: Errors I get compiling (or executing) specific packages
on the 32-bit farms (running FC8).
2. errors64.txt: Errors I get compiling (or executing) specific packages
on the 64-bit farm (running RHEL5).
3. cshrc.txt: My .cshrc file (It's well organized - should be clean to
read and diagnose the problem if there is one in there).
Any and all help is appreciated! I am onsite, so I can meet in person with
anyone who can help out.
Thanks!
Arthur A. Sabintsev
Ph.D. Student, Graduate Research Assistant
Department of Physics, The George Washington University
www.isosp.in
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####################
# General Settings #
####################
set history=1000
set savehist=1000
set noclobber
set autolist = ambiguous
umask 002
if ($?tcsh) then
setenv LINES ""
setenv COLUMNS ""
endif
#######################################
# Site-wide syslogin and sysapps File #
#######################################
source /site/env/syscshrc
source /site/env/syslogin
source /site/env/sysapps
##########################
# CLAS (CVS) Environment #
##########################
setenv ARCH uname
setenv RUN g9
setenv RUN_DIR g9frost
setenv RUN_USER arthur
setenv TOP_DIR /u/home/${RUN_USER}/clas
set cook_pass=0
set cook_version=0
setenv CVSROOT /group/clas/clas_cvs
setenv CLAS_TOOLS /group/clas/tools
setenv CLAS_PARMS /group/clas/parms
setenv CLAS_PACK /home/arthur/clas/packages
setenv CLAS_CMS ${CLAS_PACK}/cms
setenv OS_NAME "`${CLAS_CMS}/uname_clas`"
setenv CLAS_BIN "${CLAS_PACK}/../bin/${OS_NAME}"
setenv CLAS_LIB "${CLAS_PACK}/../lib/${OS_NAME}"
setenv CLAS_SLIB "${CLAS_PACK}/../slib/${OS_NAME}"
setenv CLASTOOL "${TOP_DIR}/packages/ClasTool"
echo "I am now on a ${OS_NAME} machine."
##############
# Root Setup #
##############
use root
if (${OS_NAME} == LinuxRHEL5) then
setenv CERN_ROOT /apps/cernlib/i386_rhel5/2005
setenv CERN /apps/cernlib/i386_rhel5
setenv CERN_LEVEL 2005
else if (${OS_NAME} == LinuxRHFC8) then
setenv CERN_ROOT /apps/cernlib/i386_fc8/2005
setenv CERN /apps/cernlib/i386_fc8
setenv CERN_LEVEL 2005
else if (${OS_NAME} == Linux64RHEL5) then
setenv CERN_ROOT /site/root/5.24/Linux_CentOS5.3-x86_64-gcc4.1.2
setenv CERN /site/cernlib/x86_64_rhel5/2005
setenv CERN_LEVEL 2005
endif
###############
# MySQL Setup #
###############
setenv MYSQL_INCLUDE_PATH /apps/mysql/include/mysql
setenv MYSQL_LIB_PATH /apps/mysql/lib/mysql
if ( $OS_NAME == LinuxRHFC8) then
setenv MYSQL_INCLUDE_PATH /usr/include/mysql
setenv MYSQL_LIB_PATH /usr/lib/mysql
else if ( $OS_NAME == Linux64RHEL5) then
setenv MYSQL_INCLUDE_PATH /usr/include/mysql
setenv MYSQL_LIB_PATH /usr/lib64/mysql
endif
################
# LD Libraries #
################
if ( ! $?LD_LIBRARY_PATH ) then
setenv LD_LIBRARY_PATH .
endif
if ( ! $?ins2path ) then
alias ins2path 'if (-d \!$ && "$path:q" !~ *"\!$"* ) set path=( \!$ $path )'
alias add2path 'if (-d \!$ && "$path:q" !~ *"\!$"* ) set path=( $path \!$ )'
endif
if ( ! $?add2ldpath ) then
alias add2ldpath 'if (-d \!$ && "${LD_LIBRARY_PATH}:q" !~ *"\!$"* ) setenv LD_LIBRARY_PATH "${LD_LIBRARY_PATH}:\!$" '
endif
setenv OLDPATH $PATH
setenv PATH .:$PATH
ins2path $CLAS_BIN
ins2path ${HOME}/bin/${ARCH}
add2path ${HOME}/bin/scripts
add2path ${CLASTOOL}/bin/${OS_NAME}
add2path ${CLAS_TOOLS}/caldb
add2ldpath ${HOME}/slib/${OS_NAME}
add2ldpath ${CLASTOOL}/slib/${OS_NAME}
add2path ${CERN_ROOT}/bin
####################
# g9 Database Info #
####################
setenv CSQL_DBHOST clasdb.jlab.org
setenv CSQL_DB g9_offline
setenv CSQL_TABLE pass0v0
setenv CSQL_USER offline_g9
setenv CSQL_DDL /apps/clas/parms/csql.ddl
setenv CSQL_CALIB /apps/clas/parms/calb.ddl
setenv CSQL_COMM "g9 test"
setenv CALDB_DBNAME calib
setenv CALDB_HOST clasdb.jlab.org
setenv CALDB_USER clasuser
setenv CALDB_PASS
setenv CALDB_RUNINDEX calib_user.RunIndexg9
setenv RUN_INDEX calib_user.RunIndexg9
setenv CLAS_CALDB_DBNAME calib
setenv CLAS_CALDB_HOST clasdb.jlab.org
setenv CLAS_CALDB_USER clasuser
setenv CLAS_CALDB_PASS pass0
setenv CLAS_CALDB_RUNINDEX calib_user.RunIndexg9
################
# Rootbeer 2.1 #
################
setenv ROOTBEER /u/home/arthur/rootbeer2.1
source ${ROOTBEER}/scripts/rootbeer.cshrc
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cms (32-bit):
g77 \
-O2 -mcpu=pentium -fno-automatic -finit-local-zero -ffixed-line-length-none -fno-second-underscore \
-L/u/home/arthur/clas/slib/LinuxRH8 -L/u/home/arthur/clas/lib/LinuxRH8 -L/home/arthur/clas/packages/../slib/LinuxRHFC8 -L/home/arthur/clas/packages/../lib/LinuxRHFC8 -L/apps/cernlib/i386_fc8/2005/lib -L/usr/lib/X11/.. -L/usr/lib/mysql \
-o /u/home/arthur/clas/bin/LinuxRH8/cms
g77: no input files; unwilling to write output files
make: *** [/u/home/arthur/clas/bin/LinuxRH8/cms] Error 1
Note: For some reason, there is no slib directory in /u/home/arthur/clas/. Not sure where it's supposed to come from, or how to make it.
gamecock (32-bit):
Using host libthread_db library "/lib/libthread_db.so.1".
Attaching to program: /proc/11702/exe, process 11702
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/e1/d5a85083a7d44da6056206d2c0d289a8afe73b.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/07/b722c2a7fed5b96cf4b40ce0f2a06eb0f8d2fc.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/db/a292aff9720bfc3f25c53fa8e469168460a894.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/92/8ab51a53627c59877a85dd9afecc1619ca866c.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/88/27308433e33aeefb560f42fb133577c8936f20.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/db/8cb95645d5df469d4aece301cdb5e60087be21.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/6c/1cdbb38ae2a292613c8c31195417ee80ea7e1e.debug
done.
[Thread debugging using libthread_db enabled]
[New Thread -1208523056 (LWP 11702)]
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/ba/4ea1118691c826426e9410cafb798f25cefad5.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/0a/a42d2fe3ae9510365428e8a0818d7c76401f74.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/72/500956ada6207c76c29ff8d2c555df67b7efb6.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/ac/2eeb206486bb7315d6ac4cd64de0cb50838ff6.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/a7/eabb854181ef5ff0c22b78c3e5048c64a2ebb8.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/fd/ed9da1642b1242f8fa10f35481391994499c14.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/d0/b716d925c00494a40cff204a21530d0b96df8b.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/05/21ec3b01f5c03599572e0d2598fdc0da7e21cb.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/59/42b85e278a5f1d16952fec8e1f6b3d67f2de4d.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/90/ebf9c172c9332feed316b7c0fdff30ce1a15ae.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/03/5807c541381466da2f8457545e62c87066fd4f.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/ae/c58e5f33ca51070e02528d034b00b07a890d11.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/0d/605d38e5e2d23fb14837dd95144b2d330b946c.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/7c/f32ecc91202c1747b80e3356a6828ae7ee97e7.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/13/e7ce3022231431f7402aed8afd467f81d091f0.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/67/3280e6ddac3f38973adf7b10eb773b75c69378.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/15/731d3b56abb1be2a6715ef4c7ae84a5c77564c.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/87/d66bafb3c5d1af9e5a91a447ef5efcc0a3ec3c.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/90/66503e17dcb7232b114c5878674a5932e35885.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/b8/15f4dcecb6010580bb2ebf9ad8412132353b71.debug
done.
warning: Missing the separate debug info file: /usr/lib/debug/.build-id/41/b572ad1b8e3fac8fb0dadf6bcc2b61ef6e08a9.debug
done.
0x00110402 in __kernel_vsyscall ()
#1 0x0414c953 in __waitpid_nocancel () from /lib/libc.so.6
#2 0x040f0bab in do_system () from /lib/libc.so.6
#3 0x02cc78dd in system () from /lib/libpthread.so.0
#4 0x002f622b in TUnixSystem::Exec () from /apps/root/PRO/root/lib/libCore.so.5.22
#5 0x002fbebf in TUnixSystem::StackTrace () from /apps/root/PRO/root/lib/libCore.so.5.22
#6 0x002f88be in TUnixSystem::DispatchSignals () from /apps/root/PRO/root/lib/libCore.so.5.22
#7 0x002f894c in SigHandler () from /apps/root/PRO/root/lib/libCore.so.5.22
#8 0x002f7bc9 in sighandler () from /apps/root/PRO/root/lib/libCore.so.5.22
#9 <signal handler called>
#10 0x03590381 in TGPopupMenu::AddEntry () from /apps/root/PRO/root/lib/libGui.so.5.22
#11 0x080684d4 in GoGamecock (this=0xa389840, p=0xa300670, w=1000, h=610) at gamecock.cxx:216
#12 0x0806b40f in main (argc=1, argv=0xbfe7b2a4) at gamecock.cxx:1239
The program is running. Quit anyway (and detach it)? (y or n) [answered Y; input not from terminal]
Detaching from program: /proc/11702/exe, process 11702
[1] + Terminated gamecock
Note: This error occurs when I try launching gamecock.
TPhotTiming (32-bit):
g++ -Wl,-soname,libPhotTiming.so -shared -m32 obj/LinuxRH8/TPhotTiming.o obj/LinuxRH8/TPhotTimingDict.o -o /u/home/arthur/clas/packages/ClasTool/slib/LinuxRH8/libPhotTiming.so -L/apps/root/PRO/root/lib -lPhysics -lEG -L/u/home/arthur/clas/packages/ClasTool/slib/LinuxRH8 -lClasTool -lClasBanks -lVirtualReader -lDSTReader -lMapUtils -L/home/arthur/clas/packages/../lib/LinuxRHFC8 -L/u/home/arthur/clas/lib/LinuxRH8 -fputil -lbos -lfpack -leloss -lcaldbMap -icf -lclasutil -lrecutl -lc_bos_io -ltcl -lg2c -L/apps/cernlib/i386_fc8/2005/lib -lkernlib
/usr/bin/ld: cannot find -lClasTool
collect2: ld returned 1 exit status
make: *** [/u/home/arthur/clas/packages/ClasTool/slib/LinuxRH8/libPhotTiming.so] Error 1
Note: Again, there is a dependency for the 'missing' slib directory
veff (32-bit):
make[1]: Entering directory `/u/home/arthur/clas/packages/utilities/sc_calib/veff'
test -d /u/home/arthur/clas/lib/LinuxRH8/ || mkdir -p /u/home/arthur/clas/lib/LinuxRH8/
gcc -O2 -mcpu=pentium -fwritable-strings -DLinux -I. -I/home/arthur/clas/packages/include -I/home/arthur/clas/packages/inc_derived -I/usr/include -I/usr/X11R6/include -c \
veff_calib.c -o /u/home/arthur/clas/lib/LinuxRH8/veff_calib.o
`-mcpu=' is deprecated. Use `-mtune=' or '-march=' instead.
cc1: error: unrecognized command line option "-fwritable-strings"
make[1]: *** [/u/home/arthur/clas/lib/LinuxRH8/veff_calib.o] Error 1
make[1]: Leaving directory `/u/home/arthur/clas/packages/utilities/sc_calib/veff'
make: *** [veff_calib] Error 2
Note: The first error is compiler-related.
time_walk (32-bit):
gcc -O2 -mcpu=pentium -fwritable-strings -DLinux -I. -I/home/arthur/clas/packages/include -I/home/arthur/clas/packages/inc_derived -I/usr/include -I/usr/X11R6/include -c \
make_tw_histos.c -o /u/home/arthur/clas/lib/LinuxRH8/make_tw_histos.o
`-mcpu=' is deprecated. Use `-mtune=' or '-march=' instead.
cc1: error: unrecognized command line option "-fwritable-strings"
make[1]: *** [/u/home/arthur/clas/lib/LinuxRH8/make_tw_histos.o] Error 1
make[1]: Leaving directory `/u/home/arthur/clas/packages/utilities/sc_calib/time_walk'
make: *** [make_tw_histos] Error 2
Note: Again, the first error is compiler-related.
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cms (64-bit):
Makefile:326: /home/arthur/clas/packages/cms/flags.Linux64RH5.mk: No such file or directory
Makefile:328: /home/arthur/clas/packages/cms/link.Linux64RH5.mk: No such file or directory
make: *** No rule to make target `/home/arthur/clas/packages/cms/link.Linux64RH5.mk'. Stop.
Note: Indeed, checking in the package folder shows that 'link.Linux64RH5.mk' does not exist.
gamecock (64-bit):
'/home/arthur/clas/packages/cms/Makefile:326: /home/arthur/clas/packages/cms/flags.Linux64RH5.mk: No such file or directory
/home/arthur/clas/packages/cms/Makefile:328: /home/arthur/clas/packages/cms/link.Linux64RH5.mk: No such file or directory
/home/arthur/clas/packages/cms/Makefile:661: depends/Linux64RH5/JCoupledPaddle.d: No such file or directory
/home/arthur/clas/packages/cms/Makefile:661: depends/Linux64RH5/JEventCount.d: No such file or directory
/home/arthur/clas/packages/cms/Makefile:661: depends/Linux64RH5/Jhbook2root.d: No such file or directory
Makefile:30: warning: overriding commands for target `/u/home/arthur/clas/bin/Linux64RH5/game'
/home/arthur/clas/packages/cms/Makefile:544: warning: ignoring old commands for target `/u/home/arthur/clas/bin/Linux64RH5/game'
Makefile: making dependency file for Jhbook2root.cc
/bin/sh: line 1: -pthread: command not found
Makefile: making dependency file for JEventCount.cc
/bin/sh: line 1: -pthread: command not found
Makefile: making dependency file for JCoupledPaddle.cc
/bin/sh: line 1: -pthread: command not found
make: *** No rule to make target `/home/arthur/clas/packages/cms/link.Linux64RH5.mk'. Stop.
Note: Executing 'gamecock' on a 64-bit machine doesn't work, even though I compiled it previously on a 32-bit machine. This means it needs to make connections to certain libs or flags for each OS. Therefore, when I remake gamecock, the above errors occurred.
TPhotTiming (64-bit):
g++ -Wl,-soname,libPhotTiming.so -shared -m32 obj/Linux64RH5/TPhotTiming.o obj/Linux64RH5/TPhotTimingDict.o -o /u/home/arthur/clas/packages/ClasTool/slib/Linux64RH5/libPhotTiming.so -L/apps/root/PRO/root/lib -lPhysics -lEG -L/u/home/arthur/clas/packages/ClasTool/slib/Linux64RH5 -lClasTool -lClasBanks -lVirtualReader -lDSTReader -lMapUtils -L/home/arthur/clas/packages/../lib/Linux64RHEL5 -L/u/home/arthur/clas/lib/Linux64RH5 -fputil -lbos -lfpack -leloss -lcaldbMap -icf -lclasutil -lrecutl -lc_bos_io -ltcl -lg2c -L/site/root/5.24/Linux_CentOS5.3-x86_64-gcc4.1.2/lib -lkernlib
/usr/bin/ld: cannot find -lClasTool
collect2: ld returned 1 exit status
make: *** [/u/home/arthur/clas/packages/ClasTool/slib/Linux64RH5/libPhotTiming.so] Error 1
Note: Not sure how to fix the error '/usr/bin/ld: cannot find -lClasTool'
veff (64-bit):
/home/arthur/clas/packages/cms/Makefile:326: /home/arthur/clas/packages/cms/flags.Linux64RH5.mk: No such file or directory
/home/arthur/clas/packages/cms/Makefile:328: /home/arthur/clas/packages/cms/link.Linux64RH5.mk: No such file or directory
depends/Linux64RH5/read_map.d:41: *** missing separator. Stop.
Note: Error is self-explanatory, but how do you make these links/flags?
time_walk (64-bit):
/home/arthur/clas/packages/cms/Makefile:326: /home/arthur/clas/packages/cms/flags.Linux64RH5.mk: No such file or directory
/home/arthur/clas/packages/cms/Makefile:328: /home/arthur/clas/packages/cms/link.Linux64RH5.mk: No such file or directory
depends/Linux64RH5/read_map.d:41: *** missing separator. Stop.
Note: Same error as in veff.
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