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torey
Registered: 01/21/09
Posts: 24
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 Wednesday, September 16 2009 @ 09:53 PM CEST |
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Hello,
I'm trying to do a serial install in my home directory on the HPC, just to make sure I can do that, before adding MPI.
I had problems compiling but I think those have been resolved; I was able to do a 'make' and it seemed to run ok. I had to change a 'type' variable from lowercase to uppercase in symt.c and symt_base.c in order for it to compile.
Now, however, I cannot get symt -all to execute. (I am using a tried-and-true symt.inp file). I keep getting:
-bash: symt: command not found.
I have checked and rechecked and doublechecked my .bash_profile, comparing it to the one on my Mac, and have made adjustments that I think should be correct.
Any ideas?
Thanks,
torey
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Admin
Registered: 10/12/06
Posts: 130
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| Wednesday, September 16 2009 @ 10:10 PM CEST |
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Could you show us the exact error message that makes you change the case in symt.c and symt_base.c as well as the RSPTmake.inc that you are using?
The executable symt is not in your path. Either is it some where else or else has symt not been built. Do you see any error message when you do make or does it end with the link step of rspt? What is the result of "locate symt" or "find / -name symt -print"?
/Admin |
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torey
Registered: 01/21/09
Posts: 24
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| Wednesday, September 16 2009 @ 10:38 PM CEST |
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Here is my RSPTmake.inc file:
#
# GFORTRAN/GCC with MKL
#
## COMPILERS
#
FHOME =
FCOMPILER = gfortran
FCOMPILERFLAGS = -fcray-pointer -O2 -pedantic -std=legacy
FCPPFLAGS =
FTARGETARCH =
FORTRANLIBS = -lgfortran
#FORTRANLIBS = -lifcore -lsvml -lirc -lifport -limf
F90COMPILER = gfortran
F90COMPILERFLAGS = -ffree-form
# gccCCOMPILER = gccCCOMPILERFLAGS = -O2 -std=c99
CTARGETARCH =
CPPFLAGS =
CLOADER =
FHOME =
FCOMPILER = ifort
FCOMPILERFLAGS = -O2
FCPPFLAGS =
FTARGETARCH =
#FORTRANLIBS = -lgfortran
FORTRANLIBS = -lifcore -lsvml -lirc -lifport -limf
F90COMPILER = ifort
F90COMPILERFLAGS =
# gcc
CCOMPILER = icc
CCOMPILERFLAGS = -O2 -std=c99
CTARGETARCH =
CPPFLAGS =
CLOADER =
## LIBRARIES AND INCLUDE DIRECTORIES
LAPACKLIB = -L/opt/intel/Compiler/11.0/081/mkl/lib/em64t -L/opt/intel/Compiler/11.0/081/lib/intel64 -lmkl_lapack -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lguide -lpthread
BLASLIB =
FFTWLIB = -lfftw3
EXTRALIBS =
#EXTRALIBS = -lmpi_f77
INCLUDEDIRS = -I/usr/local/include
I cannot reproduce the error message, sorry.
Here is an example of the screen after I type make, now:
make[1]: Entering directory `/lustre/home/tsemi/rsptHome/rspt480/runRspt'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/lustre/home/tsemi/rsptHome/rspt480/runRspt'
cd rsptDir; make
make[1]: Entering directory `/lustre/home/tsemi/rsptHome/rspt480/rsptDir'
cd src; make
make[2]: Entering directory `/lustre/home/tsemi/rsptHome/rspt480/rsptDir/src'
make[2]: `../../bin/rspt' is up to date.
make[2]: Leaving directory `/lustre/home/tsemi/rsptHome/rspt480/rsptDir/src'
make[1]: Leaving directory `/lustre/home/tsemi/rsptHome/rspt480/rsptDir'
Here is the result of locate symt:
warning: locate: warning: database /var/lib/slocate/slocate.db' is more than 8 days old
/lustre/home/applications/cpu2006-installed/benchspec/CPU2006/435.gromacs/src/types/symtab.h
/lustre/home/applications/cpu2006-installed/benchspec/CPU2006/435.gromacs/src/symtab.c
/lustre/home/applications/cpu2006-installed/benchspec/CPU2006/435.gromacs/src/symtab.h
/lustre/home/applications/cpu2006/benchspec/CPU2006/435.gromacs/src/types/symtab.h
/lustre/home/applications/cpu2006/benchspec/CPU2006/435.gromacs/src/symtab.c
/lustre/home/applications/cpu2006/benchspec/CPU2006/435.gromacs/src/symtab.h
/lustre/home/apps/python/2.5.2b/lib/python2.5/symtable.py
/lustre/home/apps/python/2.5.2b/lib/python2.5/symtable.pyc
/lustre/home/apps/python/2.5.2b/lib/python2.5/symtable.pyo
/lustre/home/apps/python/2.5.2b/lib/python2.5/test/test_symtable.pyc
/lustre/home/apps/python/2.5.2b/lib/python2.5/test/test_symtable.py
/lustre/home/apps/python/2.5.2b/lib/python2.5/test/test_symtable.pyo
/lustre/home/apps/python/2.5.2b/include/python2.5/symtable.h
/lustre/home/apps/compilers/src/gcc/testsuite/objc.dg/.svn/text-base/symtab-1.m.svn-base
/lustre/home/apps/compilers/src/gcc/testsuite/objc.dg/.svn/prop-base/symtab-1.m.svn-base
/lustre/home/apps/compilers/src/gcc/testsuite/objc.dg/.svn/props/symtab-1.m.svn-work
/lustre/home/apps/compilers/src/gcc/testsuite/objc.dg/symtab-1.m
/lustre/home/apps/compilers/src/libcpp/.svn/text-base/symtab.c.svn-base
/lustre/home/apps/compilers/src/libcpp/.svn/prop-base/symtab.c.svn-base
/lustre/home/apps/compilers/src/libcpp/.svn/props/symtab.c.svn-work
/lustre/home/apps/compilers/src/libcpp/include/.svn/text-base/symtab.h.svn-base
/lustre/home/apps/compilers/src/libcpp/include/.svn/prop-base/symtab.h.svn-base
/lustre/home/apps/compilers/src/libcpp/include/.svn/props/symtab.h.svn-work
/lustre/home/apps/compilers/src/libcpp/include/symtab.h
/lustre/home/apps/compilers/src/libcpp/symtab.c
/lustre/home/apps/compilers/try01/prev-libcpp/.deps/symtab.Po
/lustre/home/apps/compilers/try01/prev-libcpp/symtab.o
/lustre/home/apps/compilers/try01/libcpp/.deps/symtab.Po
/lustre/home/apps/compilers/try01/libcpp/symtab.o
/lustre/home/apps/compilers/try01/stage1-libcpp/.deps/symtab.Po
/lustre/home/apps/compilers/try01/stage1-libcpp/symtab.o
/lustre/home/gbeckham/ybomble/amber10/src/byacc/symtab.c
/lustre/home/gbeckham/ybomble/amber10/src/byacc/symtab.o
/lustre/home/gbeckham/ybomble/amber10/src/mopac6/src/symtry.f
/lustre/home/gbeckham/ybomble/amber10/src/mopac6/src/symtry.o
/lustre/home/tkaiser/bin/gdb/gdb-6.8/include/hp-symtab.h
/lustre/home/tkaiser/bin/gdb/gdb-6.8/gdb/symtab.h
/lustre/home/tkaiser/bin/gdb/gdb-6.8/gdb/testsuite/gdb.base/expand-psymtabs.exp
/lustre/home/tkaiser/bin/gdb/gdb-6.8/gdb/testsuite/gdb.base/psymtab.exp
/lustre/home/tkaiser/bin/gdb/gdb-6.8/gdb/testsuite/gdb.base/sepsymtab.c
/lustre/home/tkaiser/bin/gdb/gdb-6.8/gdb/testsuite/gdb.base/expand-psymtabs.c
/lustre/home/tkaiser/bin/gdb/gdb-6.8/gdb/testsuite/gdb.base/psymtab1.c
/lustre/home/tkaiser/bin/gdb/gdb-6.8/gdb/testsuite/gdb.base/psymtab2.c
/lustre/home/tkaiser/bin/gdb/gdb-6.8/gdb/testsuite/gdb.base/sepsymtab.exp
/lustre/home/tkaiser/bin/gdb/gdb-6.8/gdb/symtab.o
/lustre/home/tkaiser/bin/gdb/gdb-6.8/gdb/symtab.c
/lustre/home/tkaiser/pythonSrc/Python-2.5.2/Include/symtable.h
/lustre/home/tkaiser/pythonSrc/Python-2.5.2/Modules/symtablemodule.c
/lustre/home/tkaiser/pythonSrc/Python-2.5.2/Modules/symtablemodule.o
/lustre/home/tkaiser/pythonSrc/Python-2.5.2/Python/symtable.c
/lustre/home/tkaiser/pythonSrc/Python-2.5.2/Python/symtable.o
/lustre/home/tkaiser/pythonSrc/Python-2.5.2/Lib/symtable.py
/lustre/home/tkaiser/pythonSrc/Python-2.5.2/Lib/test/test_symtable.py
/lustre/home/tkaiser/petsc-2.3.3-p13/src/mat/impls/aij/seq/symtranspose.c.html
/lustre/home/tkaiser/petsc-2.3.3-p13/src/mat/impls/aij/seq/symtranspose.c
/lustre/home/asum/local/gcc/gmx-20080807/include/gromacs/symtab.h
/lustre/home/asum/local/gcc/gmx-20080807/include/gromacs/types/symtab.h
/lustre/home/ybomble/amber10/src/byacc/symtab.c
/lustre/home/ybomble/amber10/src/byacc/symtab.o
/lustre/home/ybomble/amber10/src/mopac6/src/symtry.f
/lustre/home/ybomble/amber10/src/mopac6/src/symtry.o
/lustre/home/mrwalsh/gromacs-3.3.3/src/gmxlib/.deps/symtab.Plo
/lustre/home/mrwalsh/gromacs-3.3.3/src/gmxlib/symtab.c
/lustre/home/mrwalsh/gromacs-3.3.3/src/gmxlib/symtab.o
/lustre/home/mrwalsh/gromacs-3.3.3/src/gmxlib/symtab.lo
/lustre/home/mrwalsh/gromacs-3.3.3/include/symtab.h
/lustre/home/mrwalsh/gromacs-3.3.3/include/types/symtab.h
/lustre/home/mrwalsh/grofiles/include/gromacs/symtab.h
/lustre/home/mrwalsh/grofiles/include/gromacs/types/symtab.h
/lustre/home/mrwalsh/gro2/include/gromacs/symtab.h
/lustre/home/mrwalsh/gro2/include/gromacs/types/symtab.h
/lustre/home/mrwalsh/gmx/include/types/symtab.h
/lustre/home/mrwalsh/gmx/include/symtab.h
/lustre/home/mrwalsh/gmx/src/gmxlib/symtab.c
/lustre/scratch/ddn/Python-2.5.2/Include/symtable.h
/lustre/scratch/ddn/Python-2.5.2/Modules/symtablemodule.c
/lustre/scratch/ddn/Python-2.5.2/Modules/symtablemodule.o
/lustre/scratch/ddn/Python-2.5.2/Python/symtable.c
/lustre/scratch/ddn/Python-2.5.2/Python/symtable.o
/lustre/scratch/ddn/Python-2.5.2/Lib/symtable.py
/lustre/scratch/ddn/Python-2.5.2/Lib/test/test_symtable.py
/opt/cpu2006/benchspec/CPU2006/435.gromacs/src/types/symtab.h
/opt/cpu2006/benchspec/CPU2006/435.gromacs/src/symtab.h
/opt/cpu2006/benchspec/CPU2006/435.gromacs/src/symtab.c
/opt/rocks/lib/python2.4/symtable.pyo
/opt/rocks/lib/python2.4/test/test_symtable.pyc
/opt/rocks/lib/python2.4/test/test_symtable.pyo
/opt/rocks/lib/python2.4/test/test_symtable.py
/opt/rocks/lib/python2.4/symtable.py
/opt/rocks/lib/python2.4/symtable.pyc
/opt/rocks/include/python2.4/symtable.h
/usr/lib64/python2.3/symtable.py
/usr/lib64/python2.3/test/test_symtable.py
/usr/lib64/python2.3/symtable.pyc
/usr/lib64/python2.3/symtable.pyo
/usr/include/python2.3/symtable.h
/state/partition1/home/ddn/Python-2.5.2/Lib/test/test_symtable.py
/state/partition1/home/ddn/Python-2.5.2/Lib/symtable.py
/state/partition1/home/ddn/Python-2.5.2/Modules/symtablemodule.c
/state/partition1/home/ddn/Python-2.5.2/Python/symtable.c
/state/partition1/home/ddn/Python-2.5.2/Include/symtable.h
/state/partition1/opt/cpu2006/benchspec/CPU2006/435.gromacs/src/types/symtab.h
/state/partition1/opt/cpu2006/benchspec/CPU2006/435.gromacs/src/symtab.h
/state/partition1/opt/cpu2006/benchspec/CPU2006/435.gromacs/src/symtab.c
/state/partition1/opt/rocks/lib/python2.4/symtable.pyo
/state/partition1/opt/rocks/lib/python2.4/test/test_symtable.pyc
/state/partition1/opt/rocks/lib/python2.4/test/test_symtable.pyo
/state/partition1/opt/rocks/lib/python2.4/test/test_symtable.py
/state/partition1/opt/rocks/lib/python2.4/symtable.py
/state/partition1/opt/rocks/lib/python2.4/symtable.pyc
/state/partition1/opt/rocks/include/python2.4/symtable.h
When I log on to the HPC, I get the following:
-bash: =: command not found
I don't know if that has any bearing. It used to say that it could not find RSPTHOME, so I put a $ sign in front of RSPTHOME in my .bash_profile, and that has gone away, but now this is the message.
Thank you,
torey
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Torbjorn
Registered: 11/03/06
Posts: 75
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| Thursday, September 17 2009 @ 08:49 AM CEST |
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If you get a complaint from bash on login, then your .bash_profile is likely to be corrupt in some way.
Can you write the whole .bash_profile?
If the symt program was compiled and installed properly it should be in the directory
/lustre/home/tsemi/rsptHome/rspt480/bin
Can you please run
ls /lustre/home/tsemi/rsptHome/rspt480/bin
and post the result?
Torbjörn |
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oscgr
Registered: 11/13/06
Posts: 8
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| Thursday, September 17 2009 @ 09:40 AM CEST |
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I noted that the symt files does not turn up when you try to find them. If you manage to locate symt, check if it is compiled. If it is you can do a
"export PATH=$PATH:-the path to you RSPT bin directory-"
where the symt executable is supposed to be located.
If it is not compiled, try to compile it and post the error message. Once all the paths are sorted out you can export the proper PATH in you profile.
/Oscar |
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Admin
Registered: 10/12/06
Posts: 130
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| Thursday, September 17 2009 @ 11:29 AM CEST |
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| You are using gfortran for the Fortran part but icc for the C part. Is that on purpose? You can do it that way but you have to be careful. It is often more easy to use compilers from the same family for both parts. |
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torey
Registered: 01/21/09
Posts: 24
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| Thursday, September 17 2009 @ 03:58 PM CEST |
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Torbjorn,
This is my .bash_profile; I think that you want to see it?
# .bash_profile
# Get the aliases and functions
if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi
# User specific environment and startup programs
$RSPTHOME = /lustre/home/tsemi/rsptHome/rspt480
PATH=$HOME/bin:$RSPTHOME/bin:$PATH
if [ -f /opt/intel/Compiler/11.0/081/bin/ifortvars.sh ]; then
source /opt/intel/Compiler/11.0/081/bin/ifortvars.sh intel64
fi
if [ -f /opt/intel/Compiler/11.0/081/bin/iccvars.sh ]; then
source /opt/intel/Compiler/11.0/081/bin/iccvars.sh intel64
fi
export PATH
unset USERNAME
This is what I get when I do the ls:
add2col cuthist lineg1 s2grid
addpdfiles cutout link_spts s2of
al_to_strain d2hstrain logof save
angbor d4hstrain lsfit0 sinof
arc_rename de0diff1 makealldeps smooth
areas de0diff2 make_cd_backup smooth1
atan2of density_grid makecfg smoothn
atom divide make_deltatau split
autoRef2html dosdiff makedeps split0
birmonv1 eos makefreedensity split1
birmonv2 eps_to_al makeobjs split1t
breakup evconv make_para sqrtof
bvdiff evry make_rspt_Make stick
catfirstr exkap make_ssh_backup_file stickf
cellgen expof meshparm stickf1
cellgen1 extract modpot stickfiles
cellgen2 extractrefs mtradii struc_p
cellgen3 filter0 mult struct0
checkforce0 filter1 newtau0 sttoar
checkforce1 filterm pfdiff0 sub_proto0
coastrain fit0 pi sumof
compression_grid fitls powof symform
compression_grid2 fsqrtof prepDat symt
compression_grid3 gausmooth pwdgen testdone
contodo getdatafile quadmin0 tocart
contodos getpoint rand1 towyck
conv_bir getstring randv unitcell
convdos GPa_per_mRy ref2html units
conv_dos grid reverse volume_for
conv_dos_plus grid3 rspt wordcount
convfs gsmooth runfiles wripot
conv_pdos interpol runs wriprec
conv_pdos_plus irand0 runsf wsrad
cosof kelmev runsl zeropoly
cota2 kelmry runslf
covera length_grid2 runstrs
cub less runstrsl
So, it looks like symt is in there?
Thanks,
torey |
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torey
Registered: 01/21/09
Posts: 24
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| Thursday, September 17 2009 @ 04:01 PM CEST |
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Admin-
I asked the person who is in charge of the HPC operation here for help because I could not get things to work, and this is what he suggested. I can change it back to gcc if you think it would help.
Thanks,
torey |
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Torbjorn
Registered: 11/03/06
Posts: 75
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| Thursday, September 17 2009 @ 04:07 PM CEST |
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Torey,
Your bash profile is not quite right, I think. Try to set RSPTHOME exactly like this:
RSPTHOME=/lustre/home/tsemi/rsptHome/rspt480
I removed the dollar sign and the spaces around the equals sign.
See if that helps.
Torbjörn |
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Admin
Registered: 10/12/06
Posts: 130
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| Thursday, September 17 2009 @ 04:19 PM CEST |
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You might also want to export RSPTHOME so that you can use the variable outside of the bash_profile file. Go to the top of the directory where you have the code, i.e. the directory where you can find RSPTmake.inc and do "make pristine" and then "make". If you get any error message, post it here.
/Admin
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