Thanks Mark. What I did I copied gmx from one of the servers, in which it was installed paralley.
Will have a look at your suggestions, if I get into trouble. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Feb 13, 2010 at 10:31 AM, Mark Abraham <[email protected]>wrote: > On 13/02/10 15:29, Chandan Choudhury wrote: > >> What is a cross-compiler? >> > > One that compiles an executable for architecture other than the one on > which compilation occurs. > > > My system is >> x86_64 x86_64 x86_64 GNU/Linux >> model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz >> vendor id: GenuineIntel >> > > OK, well that shouldn't be problematic. > > My next guess is that your mpicc will only compile executables that will > run with mpirun - this is a special case of cross-compilation. During the > build process, GROMACS builds the C program mknb on the compilation machine, > and then executes it normally on the compilation machine generate source > files, which are then compiled for the execution machine. However if the MPI > compiler can only generate code suitable for execution in the parallel > environment, this procedure will fail. > > In my experience, that's abnormal behaviour for mpicc - perhaps this > suggests an update of the MPI library. > > You can see if this is the problem by seeing whether you get the same issue > with ./configure --disable-mpi from a fresh copy of the GROMACS source. If > this works correctly, then you can work around the issue by running > ./configure --enable-mpi on a different fresh copy of the source, then > copying over the contents of src/gmxlib/nonbonded/nb_kernel from the > MPI-disabled version to the MPI-enabled version (perhaps then running "touch > src/gmxlib/nonbonded/nb_kernel/kernel-stamp") to make sure the Makefiles are > fooled). Now when you issue make, at the relevant point the make process > will avoid needing to run mknb. > > Another solution is to run ./configure --enable-mpi, then edit > src/gmxlib/nonbonded/nb_kernel/Makefile to correctly run mknb as a parallel > program, boot a parallel environment, then run make. > > Mark > > Chandan kumar Choudhury >> NCL, Pune >> INDIA >> >> >> On Sat, Feb 13, 2010 at 6:30 AM, Mark Abraham <[email protected] >> <mailto:[email protected]>> wrote: >> >> >> >> On 02/13/10, *Chandan Choudhury * <[email protected] >> <mailto:[email protected]>> wrote: >> >>> Hello gmx users !! >>> >>> I installed successfully installed fftw. Then tried compiling gmx >>> parallely >>> I executed the command >>> >>> $ ./configure --enable-mpi --prefix=/home/vanka/NUM-GEN/GRO/ >>> It didnot show any problem. >>> >>> $make >>> >>> make[5]: Entering directory >>> `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded/nb_kernel' >>> rm -f kernel-stamp >>> ./mknb -software_invsqrt >>> >>> make[5]: *** [kernel-stamp] Segmentation fault >>> make[5]: Leaving directory >>> `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded/nb_kernel' >>> make[4]: *** [all-recursive] Error 1 >>> make[4]: Leaving directory >>> `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded' >>> make[3]: *** [all-recursive] Error 1 >>> make[3]: Leaving directory >>> `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib' >>> make[2]: *** [all-recursive] Error 1 >>> make[2]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src' >>> make[1]: *** [all] Error 2 >>> make[1]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src' >>> make: *** [all-recursive] Error 1 >>> >> This usually means you're using a system that needs a >> cross-compiler, but since you haven't told us anything about your >> computer system, you're making everybody's life hard :-) >> >> Mark >> >>> >>> >> -- >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected] >> <mailto:[email protected]>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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