subject:"\[gmx\-users\] gromacs installation in IBM BLUEGENE"

Re: [gmx-users] gromacs installation in IBM BLUEGENE

2007-12-04 Thread Mark Abraham


Fiona Reid wrote:

Dear Anupam,

I also obtained a similar error to you when trying to install GROMACS on 
Blue Gene. I posted a message to the list on Monday but have since

found a solution.


`/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel'
rm -f kernel-stamp
./mknb   -software_invsqrt
 Gromacs nonbonded kernel generator (-h for help)
 Generating single precision functions in C.
 Using Gromacs software version of 1/sqrt(x).
Error: Cannot open nb_kernel010_c.c for writing.


Essentially the problem is that the executable ./mknb is compiled for 
the compute nodes on Blue Gene and when the make process attempts to run 
this executable on the front-end (login nodes running Linux) it fails.


I've managed to solve this problem by running ./mknb with the 
appropriate options, e.g. ./mknb -software_invsqrt for your example on 
the backend on a single processor. This enables the required 
kernel_c.c files to be created. Once the kernel files have been 
created you can continue the make process. At the final link stage you 
might encounter a number of undefined symbols, e.g. 
_nss_files_getaliasent_r and others beginning with

_nss_*

Adding -lnss_files -lnss_dns -lresolv -lc -lnss_files -lnss_dns -lresolv
to LDFLAGS should solve this problem.

Hope this helps.

Fiona


Thanks very much for that Fiona. I've added the information to the 
GROMACS Wiki here http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene


Mark
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[gmx-users] gromacs installation in IBM BLUEGENE

2007-11-28 Thread Anupam Nath Jha


Dear all

I've tried compiling both version 3.3.1 and 3.3.2 of GROMACS on an IBM Blue
Gene/L system but get the same error message with each version.

To compile the GROMACS I've used the following settings/configure flags:

./configure\
  --enable-mpi  
\
  --enable-float
\
  --program-suffix=_mpi 
\
  --prefix=/home/phd/04/mbuanjha/soft/gmx332
\
  --enable-type-prefix  
\
  --enable-all-static   
\
  --disable-nice
\
  --disable-shared  
\
  --disable-threads 
\
  --without-motif   
\
  --without-x   
\
  --without-malloc  
\
  --with-fft=fftw3  
\
  --enable-ppc-altivec  
\
  --build=i686-linux-gnu
\
  --host=powerpc
\
CC=/bgl/BlueLight/ppcfloor/bglsys/bin/mpixlc
\
   F77=/bgl/BlueLight/ppcfloor/bglsys/bin/mpixlf77  
\
   CXX=/bgl/BlueLight/ppcfloor/bglsys/bin/mpixlcxx  
\
 MPICC=/bgl/BlueLight/ppcfloor/bglsys/bin/mpixlc
\
CFLAGS=-O3 -qarch=440d -qtune=440 -qhot   
\
FFLAGS=-O3 -qarch=440d -qtune=440 -qhot   
\
  CXXFLAGS=-O3 -qarch=440d -qtune=440 -qhot   
\
   LDFLAGS=-L/home/phd/04/mbuanjha/soft/fftw312/lib/
-L/home/phd/04/mbuanjha/soft/MYINC\
  CPPFLAGS=-I/home/phd/04/mbuanjha/soft/fftw312/include/
-I/home/phd/04/mbuanjha/soft/MYINC  \
  LIBS=-lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -lcxxmpich.rts
-lnsl



at the time of running this, i got few warning, as:

configure:26419: WARNING: Couldn't find XDR headers and/or libraries - using our
own
configure:26428: checking for working memcmp
configure:26517: result: no

but when i make mdrun, it gives error:

(cd ./src/gmxlib  make ; exit 0)
make[1]: Entering directory 
`/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib'
Making all in nonbonded
make[2]: Entering directory
`/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded'
Making all in nb_kernel
make[3]: Entering directory
`/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel'
rm -f kernel-stamp
./mknb   -software_invsqrt
 Gromacs nonbonded kernel generator (-h for help)
 Generating single precision functions in C.
 Using Gromacs software version of 1/sqrt(x).
Error: Cannot open nb_kernel010_c.c for writing.
make[3]: *** [kernel-stamp] Error 1
make[3]: Leaving directory
`/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
`/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib'
(cd ./src/mdlib  make ; exit 0)
make[1]: Entering directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/mdlib'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/mdlib'
(cd ./src/kernel  make mdrun ; exit 0)
make[1]: Entering directory 
`/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/kernel'
make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by
`mdrun'.  Stop.
make[1]: Leaving directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/kernel'


and stops.

thanks in advance
anupam



-- 
Science is facts; just as houses are made of stone, so is science is made of
facts; but a pile of stones is not a house, and  a collection of facts is not
necessarily science.

Anupam Nath Jha
Ph. D. Student
Saraswathi Vishveshwara Lab
Molecular Biophysics Unit
IISc,Bangalore-560012
Karnataka
Ph. no.-22932611



-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

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Re: [gmx-users] gromacs installation in IBM BLUEGENE

2007-11-28 Thread Fiona Reid


Dear Anupam,

I also obtained a similar error to you when trying to install GROMACS 
on Blue Gene. I posted a message to the list on Monday but have since

found a solution.


`/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel'
rm -f kernel-stamp
./mknb   -software_invsqrt
 Gromacs nonbonded kernel generator (-h for help)
 Generating single precision functions in C.
 Using Gromacs software version of 1/sqrt(x).
Error: Cannot open nb_kernel010_c.c for writing.


Essentially the problem is that the executable ./mknb is compiled for the 
compute nodes on Blue Gene and when the make process attempts to run this 
executable on the front-end (login nodes running Linux) it fails.


I've managed to solve this problem by running ./mknb with the appropriate 
options, e.g. ./mknb -software_invsqrt for your example on the backend 
on a single processor. This enables the required kernel_c.c files to be 
created. Once the kernel files have been created you can continue the 
make process. At the final link stage you might encounter a number of 
undefined symbols, e.g. _nss_files_getaliasent_r and others beginning with

_nss_*

Adding -lnss_files -lnss_dns -lresolv -lc -lnss_files -lnss_dns -lresolv
to LDFLAGS should solve this problem.

Hope this helps.

Fiona
___
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Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] gromacs installation in IBM BLUEGENE

[gmx-users] gromacs installation in IBM BLUEGENE

Re: [gmx-users] gromacs installation in IBM BLUEGENE

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