<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:12pt"><div><span>It turns out the machine's Linux/glibc versions are too old. The configure passed the error after I switched to a new machine.</span></div><div><span></span> </div><div><span>Thanks a lot,</span></div><div><span>Qin</span></div><div><br></div> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 12pt;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 12pt;"> <div dir="ltr"> <div style="margin: 5px 0px; padding: 0px; border: 1px solid rgb(204, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class="hr" contentEditable="false" readonly="true"></div> <font size="2" face="Arial"> <b><span style="font-weight: bold;">From:</span></b> Barry Smith
<bsmith@mcs.anl.gov><br> <b><span style="font-weight: bold;">To:</span></b> Qin Lu <lu_qin_2000@yahoo.com> <br><b><span style="font-weight: bold;">Cc:</span></b> petsc-users <petsc-users@mcs.anl.gov> <br> <b><span style="font-weight: bold;">Sent:</span></b> Saturday, March 22, 2014 5:30 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [petsc-users] Building PETSc with Intel mpi<br> </font> </div> <div class="y_msg_container"><br><br clear="none"> There is something wrong with your environment. It is compiling the trivial program<br clear="none"><br clear="none">int main() {<br clear="none">;<br clear="none"> return 0;<br clear="none">}<br clear="none"> Pushing language C<br clear="none"> Popping language C<br clear="none">sh: mpiicc -o
/tmp/petsc-cd5uJs/config.setCompilers/conftest /tmp/petsc-cd5uJs/config.setCompilers/conftest.o <br clear="none">Executing: mpiicc -o /tmp/petsc-cd5uJs/config.setCompilers/conftest /tmp/petsc-cd5uJs/config.setCompilers/conftest.o <br clear="none">sh: <br clear="none">Executing: /tmp/petsc-cd5uJs/config.setCompilers/conftest<br clear="none">sh: /tmp/petsc-cd5uJs/config.setCompilers/conftest<br clear="none">Executing: /tmp/petsc-cd5uJs/config.setCompilers/conftest<br clear="none">sh: <br clear="none">ERROR while running executable: Could not execute "/tmp/petsc-cd5uJs/config.setCompilers/conftest":<br clear="none">/tmp/petsc-cd5uJs/config.setCompilers/conftest: error while loading shared libraries: /apps/compilers/intel_2013/impi/4.1.0.024/intel64/lib/libmpi.so.4: requires glibc 2.5 or later dynamic linker<br clear="none"><br clear="none"><br clear="none">but the resulting program cannot be run. Can you compile and run a
simple MPI program on this machine with mpiicc ? Do the following<br clear="none"><br clear="none">printf “int main(){ return 0;} > simple.c<br clear="none"><br clear="none">mpiicc -o simple simple.c <br clear="none"><br clear="none">./simplec <br clear="none"><br clear="none">does it work?<br clear="none"><br clear="none"><br clear="none"><br clear="none"><div id="yqtfd22460" class="yqt8388064255"><br clear="none">On Mar 22, 2014, at 2:24 PM, Qin Lu <<a href="mailto:lu_qin_2000@yahoo.com" shape="rect" ymailto="mailto:lu_qin_2000@yahoo.com">lu_qin_2000@yahoo.com</a>> wrote:<br clear="none"><br clear="none">> I tried what you suggested and got the following error (configure .log attached):<br clear="none">> **************<br clear="none">> sh: <br clear="none">> ERROR while running executable: Could not execute "/tmp/petsc-cd5uJs/config.setCompilers/conftest":<br clear="none">> /tmp/petsc-cd5uJs/config.setCompilers/conftest:
error while loading shared libraries: /apps/compilers/intel_2013/impi/4.1.0.024/intel64/lib/libmpi.so.4: requires glibc 2.5 or later dynamic linker<br clear="none">> ******************<br clear="none">> <br clear="none">> What can I do about this?<br clear="none">> <br clear="none">> Thanks,<br clear="none">> Qin<br clear="none">> <br clear="none">> From: Barry Smith <<a href="mailto:bsmith@mcs.anl.gov" shape="rect" ymailto="mailto:bsmith@mcs.anl.gov">bsmith@mcs.anl.gov</a>><br clear="none">> To: Qin Lu <<a href="mailto:lu_qin_2000@yahoo.com" shape="rect" ymailto="mailto:lu_qin_2000@yahoo.com">lu_qin_2000@yahoo.com</a>> <br clear="none">> Cc: petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" shape="rect" ymailto="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>> <br clear="none">> Sent: Saturday, March 22, 2014 11:46 AM<br clear="none">> Subject: Re: [petsc-users] Building
PETSc with Intel mpi<br clear="none">> <br clear="none">> <br clear="none">> On Mar 22, 2014, at 10:15 AM, Qin Lu <<a href="mailto:lu_qin_2000@yahoo.com" shape="rect" ymailto="mailto:lu_qin_2000@yahoo.com">lu_qin_2000@yahoo.com</a>> wrote:<br clear="none">> <br clear="none">> > The Intel mpi's wrappers to Intel compilers are mpiicc and mpiifort (not mpicc and mpif90), can PETSc's configure automatically pick them? Or I have to specify them explicitly (--with-cc=mpiicc --with-fc=mpiifort --with-mpi-compilers=0)?<br clear="none">> <br clear="none">> List <br clear="none">> <br clear="none">> --with-cc=mpiicc --with-fc=mpiifort <br clear="none">> <br clear="none">> do not list --with-mpi-compilers=0 or —with-mpi-dir or —with-mpi-libs<br clear="none">> <br clear="none">> Barry<br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> <br
clear="none">> > <br clear="none">> > Thanks,<br clear="none">> > Qin<br clear="none">> > <br clear="none">> > From: Satish Balay <<a href="mailto:balay@mcs.anl.gov" shape="rect" ymailto="mailto:balay@mcs.anl.gov">balay@mcs.anl.gov</a>><br clear="none">> > To: Qin Lu <<a href="mailto:lu_qin_2000@yahoo.com" shape="rect" ymailto="mailto:lu_qin_2000@yahoo.com">lu_qin_2000@yahoo.com</a>> <br clear="none">> > Cc: Barry Smith <<a href="mailto:bsmith@mcs.anl.gov" shape="rect" ymailto="mailto:bsmith@mcs.anl.gov">bsmith@mcs.anl.gov</a>>; petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" shape="rect" ymailto="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>> <br clear="none">> > Sent: Saturday, March 22, 2014 12:09 AM<br clear="none">> > Subject: Re: [petsc-users] Building PETSc with Intel mpi<br clear="none">> > <br clear="none">> > >
--with-mpi-dir=/apps/compilers/intel_2013/impi/4.1.0.024/intel64 --with-mpi-compilers=0<br clear="none">> > <br clear="none">> > Does this mpi not come with mpicc/mpif90 wrappers? If they do - its best to use them.<br clear="none">> > <br clear="none">> > If not - its best to look at the docs for this compiler - and specify it with the appropriate<br clear="none">> > <br clear="none">> > --with-mpi-include --with-mpi-lib options, [instead of the above]<br clear="none">> > <br clear="none">> > Satish<br clear="none">> > <br clear="none">> > On Fri, 21 Mar 2014, Qin Lu wrote:<br clear="none">> > <br clear="none">> > > Sourcing the .csh files of the compiler fixed the problem. Thanks! However, later it got another error (see the attached configure.log for details):<br clear="none">> > > <br clear="none">> > >
*******************************************************************************<br clear="none">> > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):<br clear="none">> > > -------------------------------------------------------------------------------<br clear="none">> > > Fortran error! mpi_init() could not be located!<br clear="none">> > > *******************************************************************************<br clear="none">> > > <br clear="none">> > > It seems the configure did not link the Intel MPI libs. I used --with-mpi-dir to specify the MPI directory, can configure get the correct Intel MPI lib names? If I have to specify the lib names (using --with-mpi-lib?), which libs should I specify? I saw a lot of libs under the directory, such as libmpi.a, libmpi_ipl64.a, libmpi_mt.a, etc. <br clear="none">> >
> <br clear="none">> > > Thanks a lot,<br clear="none">> > > Qin<br clear="none">> > > <br clear="none">> > > <br clear="none">> > > ________________________________<br clear="none">> > > From: Barry Smith <<a href="mailto:bsmith@mcs.anl.gov" shape="rect" ymailto="mailto:bsmith@mcs.anl.gov">bsmith@mcs.anl.gov</a>><br clear="none">> > > To: Qin Lu <<a href="mailto:lu_qin_2000@yahoo.com" shape="rect" ymailto="mailto:lu_qin_2000@yahoo.com">lu_qin_2000@yahoo.com</a>> <br clear="none">> > > Cc: petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" shape="rect" ymailto="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>> <br clear="none">> > > Sent: Friday, March 21, 2014 10:11 AM<br clear="none">> > > Subject: Re: [petsc-users] Building PETSc with Intel mpi<br clear="none">> > > <br clear="none">> >
> <br clear="none">> > > <br clear="none">> > > Did you follow the directions here: <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#libimf" shape="rect" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#libimf</a><br clear="none">> > > <br clear="none">> > > Did it make any difference?<br clear="none">> > > <br clear="none">> > > <br clear="none">> > > On Mar 21, 2014, at 9:45 AM, Qin Lu <<a href="mailto:lu_qin_2000@yahoo.com" shape="rect" ymailto="mailto:lu_qin_2000@yahoo.com">lu_qin_2000@yahoo.com</a>> wrote:<br clear="none">> > > <br clear="none">> > > > Hello,<br clear="none">> > > > <br clear="none">> > > > I was trying to build PETSc-3.4.2 with Intel MPI using Intel-2013 compilers in Linux, but got the error below. The configure.log is attached.<br clear="none">> > >
> <br clear="none">> > > > *******************************************************************************<br clear="none">> > > > UNABLE to EXECUTE BINARIES for ./configure <br clear="none">> > > > -------------------------------------------------------------------------------<br clear="none">> > > > Cannot run executables created with FC. If this machine uses a batch system <br clear="none">> > > > to submit jobs you will need to configure using ./configure with the additional option --with-batch.<br clear="none">> > > > Otherwise there is problem with the compilers. Can you compile and run code with your C/C++ (and maybe Fortran) compilers?<br clear="none">> > > > See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#libimf" shape="rect"
target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#libimf</a><br clear="none">> > > > *******************************************************************************<br clear="none">> > > > <br clear="none">> > > > Thanks a lot for any suggestions abut the problem,<br clear="none">> > > > <br clear="none">> > > > Regards,<br clear="none">> > > > Qin<br clear="none">> > > <br clear="none">> > > > <br clear="none">> > > > <configure.log><br clear="none">> > > <br clear="none">> > <br clear="none">> > <br clear="none">> <br clear="none">> <br clear="none">> <configure.log><br clear="none"></div><br><br></div> </div> </div> </div></body></html>