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<DIV><FONT face="Times New Roman">Dear All:</FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman">I have installed Gromacs on a Linux (RedHat)
cluster, using the following csh script - </FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT
face="Times New Roman">-------------------------------------------------------------------------------------</FONT></DIV>
<DIV><FONT size=2 face=Arial>#! /bin/csh</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>set DIR=/private/gnss/Gromacs</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>setenv SOFT ${DIR}/software<BR>setenv CPPFLAGS
"-I$SOFT/include"<BR>setenv LDFLAGS "-L$SOFT/lib"<BR>setenv NCPU 4<BR>setenv
PATH "$PATH":$SOFT/bin<BR>cd openmpi-1.2.8; ./configure --prefix=$SOFT; make -j
$NCPU; make install<BR>cd ../fftw-3.1.3; ./configure --prefix=$SOFT
--enable-float; make -j $NCPU; make install<BR>cd ../gsl-1.11; ./configure
--prefix=$SOFT; make -j $NCPU; make install<BR>cd ../gromacs-4.0.7; ./configure
--prefix=$SOFT --with-gsl; make -j $NCPU; make install<BR>make distclean;
./configure --prefix=$SOFT --program-suffix=_mpi --enable-mpi --with-gsl; make
mdrun -j $NCPU; make install-mdrun</FONT></DIV>
<DIV><FONT
face="Times New Roman">-------------------------------------------------------------------------------------</FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman">It seemed to have worked OK, and we could run
Gromacs on a single processor.</FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman">When I tried to create a parallel version with
the script -</FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV>-------------------------------------------------------------------------------------</DIV>
<DIV><FONT size=2 face=Arial>#! /bin/csh</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>set DIR=/private/gnss/Gromacs</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>setenv SOFT ${DIR}/software<BR>setenv CPPFLAGS
"-I$SOFT/include"<BR>setenv LDFLAGS "-L$SOFT/lib"<BR>setenv NCPU 4<BR>setenv
PATH "$PATH":$SOFT/bin</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>cd gromacs-4.0.7; ./configure --prefix=$SOFT
--with-gsl --enable-mpi; make -j $NCPU mdrun; make install-mdrun</FONT></DIV>
<DIV>-------------------------------------------------------------------------------------</DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman">- the installation log ended with
-</FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman">.........</FONT></DIV>
<DIV><FONT size=2 face=Arial>checking whether the MPI cc command works...
configure: error: Cannot compile and link MPI code with mpicc<BR>make: *** No
rule to make target `mdrun'. Stop.<BR>make: *** No rule to make target
`install-mdrun'. Stop.</FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman">I can't figure out from this message what is
wrong or missing with my MPI.</FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman">Can anyone help?</FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman">Thanks a lot in advance for your
help</FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman">Pinchas</FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT size=2 face=Arial>Dr. Pinchas
Aped
Tel.: (+972-3) 531-7683<BR>Department
of Chemistry
FAX : (+972-3) 738-4053<BR>Bar-Ilan
University
E-Mail: <A
href="mailto:aped@mail.biu.ac.il">aped@mail.biu.ac.il</A><BR>Ramat-Gan 52900,
ISRAEL WWW: <A
href="http://www.biu.ac.il/~aped">http://www.biu.ac.il/~aped</A><BR></FONT></DIV></BODY></HTML>