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<DIV><FONT size=2 face=Arial><SPAN class=250012309-26052010>Dear
gmx-users,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=250012309-26052010>after my
last message yesterday on the gmx-user list, I contacted the administrators
of the machine on which Gromacs 4.0.7 has been installed. We performed several
checks and concluded that probably the command mdrun_d on that machine has been
badly compiled (Gromacs has been installed in double precision), whereas the
command mdrun_mpi has been compiled correctly and works correctly. They have
some problems in finding the error in that installation because they don't know
GROMACS in details, so they would like to check the installation they made with
people more expert on GROMACS installation. I'm pasting below the steps they
made to install Gromacs 4.0.7 on this machine: :</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=250012309-26052010></SPAN></FONT> </DIV>
<DIV><SPAN class=250012309-26052010><SPAN lang=IT>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>GSL INSTALLATION:<?xml:namespace prefix = o ns =
"urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>./configure <o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>--prefix=/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gsl-19
<o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>--enable-static --enable-shared && make && make
install<o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB><o:p> </o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>FFTW INSTALLATION:<o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>./configure <o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>--prefix=/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_fftw-322
<o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>--enable-mpi --enable-static --enable-shared --enable-threads
<o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>--enable-sse2 && make && make
install<o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB><o:p> </o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>GROMACS INSTALLATION:<o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>export <o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>LDFLAGS="-L/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_fftw-322/lib
<o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>-L/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gsl-19/lib"<o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>export <o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>CPPFLAGS="-I/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_fftw-322/include
<o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>-I/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gsl-19/include"<o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>export NCPU=8<o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB><o:p> </o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>./configure <o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>--prefix=/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gromacs-407
<o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>--with-gsl --enable-shared --enable-double && make -j $NCPU
&& make <o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>install<o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB><o:p> </o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>make distclean && ./configure <o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>--prefix=/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gromacs-407
<o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt; mso-ansi-language: EN-GB"
lang=EN-GB>--program-suffix=_mpi --with-gsl --enable-mpi --enable-double
&& make <o:p></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 10pt">mdrun -j $NCPU
&& make install-mdrun</SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt"></SPAN> </P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt"></SPAN> </P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 10pt"><o:p><SPAN
class=250012309-26052010>Could anybody of you help us for the debugging of this
installation? </SPAN></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 10pt"><o:p><SPAN
class=250012309-26052010>Many thanks again and best
regards</SPAN></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"
class=MsoNormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 10pt"><o:p><SPAN
class=250012309-26052010>Anna</SPAN></o:p></SPAN></P></SPAN></SPAN></DIV>
<DIV align=left><FONT size=2
face=Arial>____________________________________________________</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Anna Marabotti, Ph.D.</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Laboratory of Bioinformatics and
Computational Biology</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Institute of Food Science,
CNR</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Via Roma, 64</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>83100 Avellino (Italy)</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Phone: +39 0825 299651</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Fax: +39 0825 781585</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Email: <A
href="mailto:anna.marabotti@isa.cnr.it">anna.marabotti@isa.cnr.it</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Skype account: annam1972</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Web page: <A
href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial></FONT> </DIV>
<DIV align=left><FONT size=2 face=Arial>"If you think you are too small to make
a difference, try sleeping with a mosquito"</FONT></DIV>
<DIV> </DIV></BODY></HTML>