Thanks Mark.<br>What I did I copied gmx from one of the servers, in which it was installed paralley.<br><br>Will have a look at your suggestions, if I get into trouble.<br><br>Chandan<br clear="all"><br>--<br>Chandan kumar Choudhury<br>
NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Sat, Feb 13, 2010 at 10:31 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">On 13/02/10 15:29, Chandan Choudhury wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
What is a cross-compiler?<br>
</blockquote>
<br></div>
One that compiles an executable for architecture other than the one on which compilation occurs.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
My system is<br>
x86_64 x86_64 x86_64 GNU/Linux<br>
model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz<br>
vendor id: GenuineIntel<br>
</blockquote>
<br></div>
OK, well that shouldn't be problematic.<br>
<br>
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.<br>
<br>
In my experience, that's abnormal behaviour for mpicc - perhaps this suggests an update of the MPI library.<br>
<br>
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.<br>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
Chandan kumar Choudhury<br>
NCL, Pune<br>
INDIA<br>
<br>
<br>
On Sat, Feb 13, 2010 at 6:30 AM, Mark Abraham <<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a><br></div><div class="im">
<mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>>> wrote:<br>
<br>
<br>
<br>
On 02/13/10, *Chandan Choudhury * <<a href="mailto:iitdckc@gmail.com" target="_blank">iitdckc@gmail.com</a><br></div><div><div></div><div class="h5">
<mailto:<a href="mailto:iitdckc@gmail.com" target="_blank">iitdckc@gmail.com</a>>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello gmx users !!<br>
<br>
I installed successfully installed fftw. Then tried compiling gmx<br>
parallely<br>
I executed the command<br>
<br>
$ ./configure --enable-mpi --prefix=/home/vanka/NUM-GEN/GRO/<br>
It didnot show any problem.<br>
<br>
$make<br>
<br>
make[5]: Entering directory<br>
`/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded/nb_kernel'<br>
rm -f kernel-stamp<br>
./mknb -software_invsqrt<br>
<br>
make[5]: *** [kernel-stamp] Segmentation fault<br>
make[5]: Leaving directory<br>
`/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded/nb_kernel'<br>
make[4]: *** [all-recursive] Error 1<br>
make[4]: Leaving directory<br>
`/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded'<br>
make[3]: *** [all-recursive] Error 1<br>
make[3]: Leaving directory<br>
`/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib'<br>
make[2]: *** [all-recursive] Error 1<br>
make[2]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src'<br>
make[1]: *** [all] Error 2<br>
make[1]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src'<br>
make: *** [all-recursive] Error 1<br>
</blockquote>
This usually means you're using a system that needs a<br>
cross-compiler, but since you haven't told us anything about your<br>
computer system, you're making everybody's life hard :-)<br>
<br>
Mark<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
</blockquote>
<br>
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