open-mpi gromacs problem...

[ramadavid]

Hi Fedora friends,

I a novice to the Fedora.
I install Gromacs from fedora add-remove software package.

I also install open-mpi.
Now when i am try to invoke openmpi with command
mpirun ...Fedora respons with No such coomand ..

I am not able to understand these reason. gromacs is also unable to run on
parallel (g_mdrun_mpi command not working.. though add-remove software say gromacs is complile with mpi ). Groamac is working on threads...

Please tell me how to invoke mpi ( openmpi) to parallel processing??

[tashirosgt]

Originally Posted by ramadavid

Now when i am try to invoke openmpi with command
mpirun ...Fedora respons with No such coomand ..

Try using the complete path to the command. I don't know what the complete path is. It might be something like
/usr/bin/mpirun -h

[ramadavid]

THANK YOU for reply..

The gromacs compile with open-mpi should work on
multiple nodes ...( g_mdrun_mpi) .These is also mention in add/remove software
package.But unfortunatly, gromacs is not compile with open-mpi to run on multinodes..
It is working on single node, the add/remove software package of FEDORA- 17 is telling a different thing. So its my request to help me is the software package is wrong or am I????
When I look in /usr/bin I can found all other command of gromacs but not g_mdrun_mpi...


Thank you in advance..
With best wishes and regards.

[tashirosgt]

Let me restate your situation for you.

You wish to use the gromacs software http://www.gromacs.org/, which deals with molecular dynamics. You want to run this software in parallel mode using the Open MPI software http://www.open-mpi.org/. I assume this is your thread on the gromacs mailing list:http://lists.gromacs.org/pipermail/g...ly/073605.html. You say that both these packages can be installed in Fedora using yum. (You didn't mention which version of Fedora.) However, you say that the version of growmacs installed by yum is not capable of using Open MPI. The response that you got on the mailing list is that the Fedora packages are not supported by the gromacs team, so they do not know capability of the Fedora versions. The reply advises you to compile gromacs from source.

Originally Posted by ramadavid

The gromacs compile with open-mpi should work on
multiple nodes ...( g_mdrun_mpi) .These is also mention in add/remove software
package.But unfortunatly, gromacs is not compile with open-mpi to run on multinodes..

Are you saying that you compiled gromacs from source code and that the resulting executable is not capable of using Open MPI ?

It is working on single node, the add/remove software package of FEDORA- 17 is telling a different thing. So its my request to help me is the software package is wrong or am I????

Are you talking about the "add/remove" gui interface? How is this "telling" you anything? (I haven't installed growmacs, so I don't know what annotations it might be showing you about it.)

[ramadavid]

Thank you for reply,

Yes you are right that fedora packages are not supported by Gromacs team..

I am using fedora 17. Add/remove software package is telling that Groamcs open-mpi binaries and libraries are compile to run on thread and Open-mpi( multiple nodes).
It is working on multithread but not on openmpi ( multiple nodes)...

So I am wonder what is the problem..????

is I miss something,then please tell me..

I am a novice to linux..

Thank you in advance

With best wishes and regards..

---------- Post added at 05:19 PM ---------- Previous post was at 04:49 PM ----------

Hi Fedora Friends

I am trying to install gromacs 4.5.4 in parallel operating system fedora 17
I am using dell T 3500 precision , 6C.

I downloaded openmppi-1.6
Command line to install
./configure --prefix=/usr/local
make all install

For fftw 3.3.2 installation command line was .

./configure --enable-float
make
make install

To Gromacs I wrote..
./configure --enable-mpi --with-fft=fftw3 --program-suffix=_mpi


System reply with
configure error : cannot compute sizeof ( off_t)...

config .log show following error...It very big..I am pesting only a
small part...

Please tell me the reason for such error ...?? And how to overcome these???
.
.
.
.
.
.
configure:5529: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.5.4"
| #define PACKAGE_STRING "gromacs 4.5.4"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
| #define PACKAGE_URL ""
| #define PACKAGE "gromacs"
| #define VERSION "4.5.4"
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME "Tue Aug 7 10:46:37 IST 2012"
| #define BUILD_MACHINE "Linux 3.5.0-2.fc17.x86_64 x86_64"
| #define GMX_MPI /**/
| #define GMX_LIB_MPI /**/
| #define MPI_IN_PLACE_EXISTS /**/
| /* end confdefs.h. */
|
| #if defined __QK_USER__
| #else
| #error not catamount
| #endif
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:5551: result: no
configure:6229: checking how to run the C preprocessor
configure:6260: mpicc -E -I/usr/local/lib conftest.c
configure:6260: $? = 0
configure:6274: mpicc -E -I/usr/local/lib conftest.c
conftest.c:22:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:6274: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.5.4"
| #define PACKAGE_STRING "gromacs 4.5.4"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
| #define PACKAGE_URL ""
| #define PACKAGE "gromacs"
| #define VERSION "4.5.4"
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME "Tue Aug 7 10:46:37 IST 2012"
| #define BUILD_USER "prashant@prashant"
| #define BUILD_MACHINE "Linux 3.5.0-2.fc17.x86_64 x86_64"
| #define GMX_MPI /**/
| #define GMX_LIB_MPI /**/
| #define MPI_IN_PLACE_EXISTS /**/
| #define F77_OR_C_FUNC(name,NAME) name
| #define F77_OR_C_FUNC_(name,NAME) name
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:6299: result: mpicc -E
configure:6319: mpicc -E -I/usr/local/lib conftest.c
configure:6319: $? = 0
configure:6333: mpicc -E -I/usr/local/lib conftest.c
conftest.c:22:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:6333: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.5.4"
| #define PACKAGE_STRING "gromacs 4.5.4"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
| #define PACKAGE_URL ""
| #define PACKAGE "gromacs"
| #define VERSION "4.5.4"
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME "Tue Aug 7 10:46:37 IST 2012"
| #define BUILD_USER "prashant@prashant"
| #define BUILD_MACHINE "Linux 3.5.0-2.fc17.x86_64 x86_64"
| #define GMX_MPI /**/
| #define GMX_LIB_MPI /**/
| #define MPI_IN_PLACE_EXISTS /**/
| #define F77_OR_C_FUNC(name,NAME) name
| #define F77_OR_C_FUNC_(name,NAME) name
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:6362: checking for grep that handles long lines and -e
configure:6420: result: /usr/bin/grep
configure:6425: checking for egrep
configure:6487: result: /usr/bin/grep -E
configure:6492: checking whether ln -s works
configure:6496: result: yes
configure:6895: checking whether mpicc accepts -O3
configure:6913: result: yes
configure:7193: checking whether mpicc accepts -msse2
configure:7211: result: yes
configure:7225: checking whether mpicc accepts -funroll-all-loops
configure:7243: result: yes
configure:7255: checking whether mpicc accepts -std=gnu99
configure:7273: result: yes
configure:7288: checking whether mpicc accepts -fexcess-precision=fast
configure:7306: result: yes
configure:7347: checking whether mpicc accepts -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -fexcess-precision=fast
configure:7365: result: yes
configure:8089: checking whether byte ordering is bigendian
configure:8104: mpicc -c -O3 -fomit-frame-pointer -finline-functions
-Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99
-fexcess-precision=fast -I/usr/local/lib conftest.c >&5
conftest.c:23:9: error: unknown type name 'not'
conftest.c:23:15: error: expected '=', ',', ';', 'asm' or
'__attribute__' before 'universal'
conftest.c:23:15: error: unknown type name 'universal'
configure:8104: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.5.4"
| #define PACKAGE_STRING "gromacs 4.5.4"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
| #define PACKAGE_URL ""
| #define PACKAGE "gromacs"
| #define VERSION "4.5.4"
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME "Tue Aug 7 10:46:37 IST 2012"
| #define BUILD_USER "prashant@prashant"
| #define BUILD_MACHINE "Linux 3.5.0-2.fc17.x86_64 x86_64"
| #define GMX_MPI /**/
| #define GMX_LIB_MPI /**/
| #define MPI_IN_PLACE_EXISTS /**/
| #define F77_OR_C_FUNC(name,NAME) name
| #define F77_OR_C_FUNC_(name,NAME) name
| /* end confdefs.h. */
| #ifndef __APPLE_CC__
| not a universal capable compiler
| #endif
| typedef int dummy;
|
configure:8157: mpicc -c -O3 -fomit-frame-pointer -finline-functions
-Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99
-fexcess-precision=fast -I/usr/local/lib conftest.c >&5
configure:8157: $? = 0
configure:8183: mpicc -c -O3 -fomit-frame-pointer -finline-functions
-Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99
-fexcess-precision=fast -I/usr/local/lib conftest.c >&5
conftest.c: In function 'main':
conftest.c:37:4: error: unknown type name 'not'
conftest.c:37:12: error: expected '=', ',', ';', 'asm' or
'__attribute__' before 'endian'
configure:8183: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.5.4"
| #define PACKAGE_STRING "gromacs 4.5.4"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
| #define PACKAGE_URL ""
| #define PACKAGE "gromacs"
| #define VERSION "4.5.4"
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME "Tue Aug 7 10:46:37 IST 2012"
.
.
.
.
.
.
.



configure error : cannot compute sizeof ( off_t)...



Thank you ...

With best wishes and regards...

[ramadavid]

Hi fedora friends,

I tried in another way .
I install the openmpi1.6 and fftw3.3.2 to the /opt/openmpi-1.6 and /opt/fftw-3.3.2.
respectivly

at the time of make (for gromacs) I encouner with error suggesting to
recompile with -fPIC..

As per instruction on gromacs website, I added glag --enable-shared to the
fftw, but again at the time of
gromacs configuration I encounter the sane error suggesting to
recompile with -fPIC


So I used following coomand line ( as per instruction on gromacs website)

./configure --with-fft=fftw3 --enable-mpi --program-suffix=_mpi
--prefix=/opt/gmx_4.5.4 --disable-shared

make
make install
make tests
make links

make install-mdrun
make links
output .....


Libraries have been installed in:
/opt/gmx_4.5.4/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,--rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
test -z "/opt/gmx_4.5.4/lib/pkgconfig" || /usr/bin/mkdir -p
"/opt/gmx_4.5.4/lib/pkgconfig"
/usr/bin/install -c -m 644 libgmx_mpi.pc '/opt/gmx_4.5.4/lib/pkgconfig'
make[3]: Leaving directory `/opt/gromacs-4.5.4/src/gmxlib'
make[2]: Leaving directory `/opt/gromacs-4.5.4/src/gmxlib'
make[1]: Leaving directory `/opt/gromacs-4.5.4/src/gmxlib'
(cd ./src/mdlib && make install ; exit 0)
make[1]: Entering directory `/opt/gromacs-4.5.4/src/mdlib'
make[2]: Entering directory `/opt/gromacs-4.5.4/src/mdlib'
test -z "/opt/gmx_4.5.4/lib" || /usr/bin/mkdir -p "/opt/gmx_4.5.4/lib"
/bin/sh ../../libtool --mode=install /usr/bin/install -c
libmd_mpi.la '/opt/gmx_4.5.4/lib'
/usr/bin/install -c .libs/libmd_mpi.lai /opt/gmx_4.5.4/lib/libmd_mpi.la
/usr/bin/install -c .libs/libmd_mpi.a /opt/gmx_4.5.4/lib/libmd_mpi.a
chmod 644 /opt/gmx_4.5.4/lib/libmd_mpi.a
ranlib /opt/gmx_4.5.4/lib/libmd_mpi.a
PATH="$PATH:/sbin" ldconfig -n /opt/gmx_4.5.4/lib
----------------------------------------------------------------------
Libraries have been installed in:
/opt/gmx_4.5.4/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,--rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
test -z "/opt/gmx_4.5.4/lib/pkgconfig" || /usr/bin/mkdir -p
"/opt/gmx_4.5.4/lib/pkgconfig"
/usr/bin/install -c -m 644 libmd_mpi.pc '/opt/gmx_4.5.4/lib/pkgconfig'
make[2]: Leaving directory `/opt/gromacs-4.5.4/src/mdlib'
make[1]: Leaving directory `/opt/gromacs-4.5.4/src/mdlib'
(cd ./src/kernel && make install-libLTLIBRARIES ; exit 0)
make[1]: Entering directory `/opt/gromacs-4.5.4/src/kernel'
test -z "/opt/gmx_4.5.4/lib" || /usr/bin/mkdir -p "/opt/gmx_4.5.4/lib"
/bin/sh ../../libtool --mode=install /usr/bin/install -c
libgmxpreprocess_mpi.la '/opt/gmx_4.5.4/lib'
/usr/bin/install -c .libs/libgmxpreprocess_mpi.lai
/opt/gmx_4.5.4/lib/libgmxpreprocess_mpi.la
/usr/bin/install -c .libs/libgmxpreprocess_mpi.a
/opt/gmx_4.5.4/lib/libgmxpreprocess_mpi.a
chmod 644 /opt/gmx_4.5.4/lib/libgmxpreprocess_mpi.a
ranlib /opt/gmx_4.5.4/lib/libgmxpreprocess_mpi.a
PATH="$PATH:/sbin" ldconfig -n /opt/gmx_4.5.4/lib
----------------------------------------------------------------------
Libraries have been installed in:
/opt/gmx_4.5.4/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,--rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[1]: Leaving directory `/opt/gromacs-4.5.4/src/kernel'
(cd ./src/kernel && make install-mdrun ; exit 0)
make[1]: Entering directory `/opt/gromacs-4.5.4/src/kernel'
/bin/sh ../../config/mkinstalldirs /opt/gmx_4.5.4/bin
if test -f mdrun; then \
f=`echo mdrun|sed 's/$//;s&$&_mpi&;s/$//'`; \
echo " /bin/sh ../../libtool --mode=install /usr/bin/install -c
mdrun /opt/gmx_4.5.4/bin/$f"; \
/bin/sh ../../libtool --mode=install /usr/bin/install -c mdrun
/opt/gmx_4.5.4/bin/$f; \
else :; fi
/bin/sh ../../libtool --mode=install /usr/bin/install -c mdrun
/opt/gmx_4.5.4/bin/mdrun_mpi
/usr/bin/install -c mdrun /opt/gmx_4.5.4/bin/mdrun_mpi
make[1]: Leaving directory `/opt/gromacs-4.5.4/src/kernel'
[root@prashant gromacs-4.5.4]# make links
cd /opt/gmx_4.5.4/bin && programs=`ls` && cd /usr/local/bin && \
for i in $programs; do \
(test ! -f $i && ln -s /opt/gmx_4.5.4/bin/$i . ; exit 0); \
done


When I am giving the command
pdb2gmx_mpi
pdb2gmx_mpi: error while loading shared libraries: libmpi.so.1: cannot
open shared object file: No such file or directory


I have a small experience in linux only, That why I may be missing or
done something wrong???
So please tell me where is the problem ????

Thank you in advane..
With best wishes and regards

Rama david

[tashirosgt]

You need to explain what exactly what the add/remove software program reported. (It is isn't the add/remove software "package".) Many experienced Linux users never use add/remove software because they accomplish such tasks by runnng the command "yum" from a terminal. If you say that add/remove software "tells" you something, it is not clear what you mean.

I ran the add/remove software program and searched for "gromacs". Now I understand that the packages have annotations which appear in a text window. For growmacs, we find the followng annotation:

GROMACS is a versatile and extremely well optimized package to perform molecular dynamics computer simulations and subsequent trajectory analysis. It is developed for biomolecules like proteins, but the extremely high performance means it is used also in several other field like polymer chemistry and solid state physics.
This package provides single and double precision binaries. The documentation is in the package gromacs-common.
mdrun has been compiled with thread parallellization, so it runs in parallel on shared memory systems. If you want to run on a cluster, you probably want to install one of the MPI parallellized packages.
N.B. All binaries have names starting with g, for example mdrun has been renamed to gmdrun.

What package has annotations that say it is an MPII parallelized?

---------- Post added at 07:27 PM ---------- Previous post was at 11:01 AM ----------

Are you familiar with makefiles and do you roughly understand how the "configure" process works? You said you aren't experienced in Linux, but have you used Unix?

When I am giving the command
pdb2gmx_mpi
pdb2gmx_mpi: error while loading shared libraries: libmpi.so.1: cannot
open shared object file: No such file or directory

The first thing to do is to find out if the file libmpi.so.1 is somewhere on your machine.

One way to do that is (as root) to do

updatedb

When that finishes, do (as an ordinary user, if you wish)

locate libmpi.so.1

[ramadavid]

Thank you for reply andyour pations to listen me..


Groamcs open MPI binaries and libraries (add/remove software program)
Annotation..
GROMACS is a versatile and extremely well optimized package to perform molecular dynamics computer simulations and subsequent trajectory analysis. It is developed for biomolecules like proteins, but the extremely high performance means it is used also in several other field like polymer chemistry and solid state physics.
mdrun has been compiled with thread parallellization (for running on a single node) and with Open MPI (for running on multiple nodes). This package single and double precision binaries and libraries.


After giving the command
updatedb

locate libmpi.so.1

root@prashant opt]# locate libmpi.so.1
/home/prashant/Desktop/software/openmpi/openmpi-1.6/ompi/.libs/libmpi.so.1
/home/prashant/Desktop/software/openmpi/openmpi-1.6/ompi/.libs/libmpi.so.1.0.3
/opt/openmpi-1.6/lib/libmpi.so.1
/opt/openmpi-1.6/lib/libmpi.so.1.0.3
/opt/openmpi-1.6/ompi/.libs/libmpi.so.1
/opt/openmpi-1.6/ompi/.libs/libmpi.so.1.0.3
/usr/local/lib/libmpi.so.1
/usr/local/lib/libmpi.so.1.0.3



But after giving the command pdb2gmx_mpi ..I stuck with the same problem
pdb2gmx_mpi: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory

Please give me suggestion to solve problem

With best wishes and regards

Rama david

[tashirosgt]

I'm not positive what causes the error, but perhaps this message from the log file is relevant.

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,--rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.

I am not sure whether the pdb2gmx_mpi actually invokes the command "ld" to load libraries, but if it does then it must be told where the library files are. The man page for pdb2gmx_mpi may tell you this and it may explain how to include the path to the library files by using options with the command pdb2gmx_mpi.

See if

 
man pdb2gmx_mpi

explains anything.

You should become aware of your "environmental variables" when doing command line work. The command

env

will display them.

You can examine the value of a single environmental variable such as HOME by the command

echo $HOME

(The dollar sign is necessary. Roughly speaking, it means "use the value of the variable".)

You can establish a variable called LD_LIBRARY_PATH if there is none present, by

LD_LIBRARY_PATH="/opt/openmpi-1.6/lib"

(No dollar sign in front of LD_LIBRARY_PATH is used in this command.)

Do that and then try the pdb2gmx_mpi command and see if the error message is different.

Setting the variable LD_LIBRARY_PATH will not be permanent. It won't exist when you login again or open a new terminal. To set it permanently, you can edit the .bash_profile or .bashrc file in your home directory. But I suggest we don't do that until we find out if LD_LIBRARY_PATH is relevant to your problem.

[ramadavid]

Thank you a lot for your HELP and patience ...

LD_LIBRARY_PATH="/opt/openmpi-1.6/lib"

Solve my problem ..

What is next step...

What i have to edit in .bashrc file or bash_profile????

( I also try by adding export LD_LIBRARY_PATH="/opt/openmpi-1.6/lib" ..But on the new shell the error repeat)

Thank again to listen me well..

Please would you suggest me some links to read these topics
as I am novice to linux...???
These would be a great help to me..


With best wishes and regards..

Rama david

---------- Post added at 11:36 AM ---------- Previous post was at 08:14 AM ----------

Hi Fedora Friends...

I am using fedora 17..And I install gromacs software iin /usr/local

When I gave command pdb2gmx_mpi I got the error like.... error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory


Butw when I execute the following commands.....I get the access to gromacs
export LD_LIBRARY_PATH="/opt/opempi-1.6/lib"

PATH=/usr/local/gromacs/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/home/prashant/.local/bin:/home/prashant/bin:/opt/opempi-1.6/lib



But when I open the new shell, I have to give these two commands to get access to software..

So please help me in these regards ..

How to set permanent solution to avoid inconvenience??



Thank you in advance...

With best wishes and regards..
Rama david..

[tashirosgt]

I have only superficially glanced at some web pages about the bash shell this morning. This one looks OK: http://tille.garrels.be/training/bash/ch03.html

Edits to your .bashrc and .bash_profile files won't take effect until you log out and log back in.

I think you should set your LD_LIBRARY_PATH in the .bash_profile file. The function of the two files is explained on the page: http://www.joshstaiger.org/archives/...rofile_vs.html

[ramadavid]

Thank you a lot for help..

I added path and LD_LIBRARY_PATH to the .bashrc file..

It solve all the problem...
Thank you a lot for your patience to hear and a giving suggestion

I have another query...Suppose now i install another new software and it also needed the LD_LIBRARY_PATH then in such condition should I need to modify the .bashrc file again
with new LD_LIBRARY_PATH ... will it affect my gromacs installation???

Thank you a lot for suggestion...


With Best wishes and regards..
Rama david

[tashirosgt]

LD_LIBRARY_PATH can be set to a list of directories separated by colons. It doesn't have to be merely a single directory.



A standard way of modifying a path variable is to add another directory to the list. If you wanted to add the directory /user/bin/newdir to LD_LIBRARY_PATH you could do it by:

LD_LIBRARY_PATH = $LD_LIBRARY_PATH:"/user/bin/newdir"