<div dir="ltr"><div class="gmail_default" style="font-size:small">Thanks for checking. </div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default">My program is coded with C++ actually, so fortran may not be necessary. I compiled PETSc on our university cluster, where a MPI package has already been installed as universal module. It seems not compatible with PETSc. So I am trying to install my own version of MPI and link it to PETSc. </div><div class="gmail_default"><br></div><div class="gmail_default" style="font-size:small">As compile PETSc using its default configuration, it automatically downloaded the mpi . </div><div class="gmail_default" style="font-size:small"><span style="background-color:rgb(213,234,255);color:rgb(255,0,0);font-family:Pragmata,Menlo,'DejaVu LGC Sans Mono','DejaVu Sans Mono',Consolas,'Everson Mono','Lucida Console','Andale Mono','Nimbus Mono L','Liberation Mono',FreeMono,'Osaka Monospaced',Courier,'New Courier',monospace;font-size:14.666666984558105px">./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack --download-mpich</span><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">I was wondering if it does the same thing as I installed MPI by my own.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">Thanks again.</div><div class="gmail_default" style="font-size:small">Paul</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div style="color:rgb(0,0,0)"><font size="1">Huaibao (Paul) Zhang<br><b><i>Gas Surface Interactions Lab</i></b><br></font></div>
<div style="color:rgb(0,0,0)"><font size="1">Department of Mechanical Engineering</font></div>
<div style="color:rgb(0,0,0)"><font size="1">University of Kentucky,</font></div>
<div style="color:rgb(0,0,0)"><font size="1">Lexington,</font></div>
<div style="margin:0px;font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;line-height:normal;font-size-adjust:none;font-stretch:normal"><font size="1">KY, 40506-0503<b><br>Office</b>: 216 Ralph G. Anderson Building<br><b>Web</b>:<a href="http://gsil.engineering.uky.edu" target="_blank"><span style="color:rgb(0,0,153)">gsil.engineering.uky.edu</span></a></font><span style="color:rgb(0,0,0)"><span style="color:rgb(0,0,153)"></span></span></div><div style="color:rgb(255,102,102)"><font size="1"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="font-family:Tahoma"><span style="font-family:Verdana"><font face="Helvetica"><span></span></font></span></span></span></span></span></span></span></font></div></div></div>
<br><div class="gmail_quote">On Mon, Dec 1, 2014 at 2:06 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><span class="">On Mon, Dec 1, 2014 at 1:02 PM, paul zhang <span dir="ltr"><<a href="mailto:paulhuaizhang@gmail.com" target="_blank">paulhuaizhang@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div style="font-size:small">I should have installed openmpi successfully...</div></div></blockquote><div><br></div></span><div>The Fortran wrapper does not seem to correctly link the libraries:</div><div><br></div><div><div>ERROR while running executable: Could not execute "/tmp/petsc-rVaKfJ/config.setCompilers/conftest":</div><div>/tmp/petsc-rVaKfJ/config.setCompilers/conftest: symbol lookup error: /home/hzh225/LIB_CFD/openmpi-1.8.3/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty</div></div><div><br></div><div>Or else you need something in your LD_LIBRARY_PATH. Either way, so you need Fortran? If so,</div><div>use --download-mpich, otherwise use --with-fc=0.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div><div class="h5"><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div style="font-size:small">Attached. </div><div style="font-size:small"><br>Thanks,<br>Paul</div></div><div class="gmail_extra"><br clear="all"><div><div><div style="color:rgb(0,0,0)"><font size="1">Huaibao (Paul) Zhang<br><b><i>Gas Surface Interactions Lab</i></b><br></font></div>
<div style="color:rgb(0,0,0)"><font size="1">Department of Mechanical Engineering</font></div>
<div style="color:rgb(0,0,0)"><font size="1">University of Kentucky,</font></div>
<div style="color:rgb(0,0,0)"><font size="1">Lexington,</font></div>
<div style="margin:0px;font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;line-height:normal;font-stretch:normal"><font size="1">KY, 40506-0503<b><br>Office</b>: 216 Ralph G. Anderson Building<br><b>Web</b>:<a href="http://gsil.engineering.uky.edu" target="_blank"><span style="color:rgb(0,0,153)">gsil.engineering.uky.edu</span></a></font><span style="color:rgb(0,0,0)"><span style="color:rgb(0,0,153)"></span></span></div><div style="color:rgb(255,102,102)"><font size="1"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="font-family:Tahoma"><span style="font-family:Verdana"><font face="Helvetica"><span></span></font></span></span></span></span></span></span></span></font></div></div></div>
<br><div class="gmail_quote">On Mon, Dec 1, 2014 at 1:59 PM, Barry Smith <span dir="ltr"><<a href="mailto:bsmith@mcs.anl.gov" target="_blank">bsmith@mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><br>
Send configure.log for the ./configure with<br>
<span><br>
./configure --download-fblaslapack --with-valgrind-dir=/share/cluster/RHEL6.2/x86_64/apps/valgrind/3.9.0 --with-mpi=1 --with-mpi-dir=/home/hzh225/LIB_CFD/openmpi-1.8.3<br>
<br>
<br>
</span><span><font color="#888888">Barry<br>
</font></span><div><div><br>
<br>
> On Dec 1, 2014, at 12:55 PM, paul zhang <<a href="mailto:paulhuaizhang@gmail.com" target="_blank">paulhuaizhang@gmail.com</a>> wrote:<br>
><br>
> Matt,<br>
><br>
> Sorry to poke you again. I am in a dilemma.<br>
><br>
> If I use<br>
><br>
> ./configure --with-cc=mpicc --with-cxx=mpiCC --with-fc=mpif77 --download-fblaslapack --with-valgrind-dir=/share/cluster/RHEL6.2/x86_64/apps/valgrind/3.9.0 --with-mpi=1 --with-mpi-dir=/home/hzh225/LIB_CFD/openmpi-1.8.3/<br>
><br>
><br>
> Then I am told to<br>
><br>
> TESTING: checkMPICompilerOverride from config.setCompilers(config/BuildSystem/config/setCompilers.py:1501) *******************************************************************************<br>
> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):<br>
> -------------------------------------------------------------------------------<br>
> --with-cc=mpicc is specified with --with-mpi-dir=/home/hzh225/LIB_CFD/openmpi-1.8.3. However /home/hzh225/LIB_CFD/openmpi-1.8.3/bin/mpicc exists and should be the prefered compiler! Suggest not specifying --with-cc option so that configure can use /home/hzh225/LIB_CFD/openmpi-1.8.3/bin/mpicc instead.<br>
> *******************************************************************************<br>
><br>
><br>
> However if I skip those compilers,<br>
><br>
> ./configure --download-fblaslapack --with-valgrind-dir=/share/cluster/RHEL6.2/x86_64/apps/valgrind/3.9.0 --with-mpi=1 --with-mpi-dir=/home/hzh225/LIB_CFD/openmpi-1.8.3<br>
><br>
><br>
> My problem now is<br>
><br>
> ===============================================================================<br>
> Configuring PETSc to compile on your system<br>
> ===============================================================================<br>
> TESTING: checkFortranCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:910) *******************************************************************************<br>
> UNABLE to EXECUTE BINARIES for ./configure<br>
> -------------------------------------------------------------------------------<br>
> Cannot run executables created with FC. If this machine uses a batch system<br>
> to submit jobs you will need to configure using ./configure with the additional option --with-batch.<br>
> Otherwise there is problem with the compilers. Can you compile and run code with your C/C++ (and maybe Fortran) compilers?<br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
> Huaibao (Paul) Zhang<br>
> Gas Surface Interactions Lab<br>
> Department of Mechanical Engineering<br>
> University of Kentucky,<br>
> Lexington,<br>
> KY, 40506-0503<br>
> Office: 216 Ralph G. Anderson Building<br>
> Web:<a href="http://gsil.engineering.uky.edu" target="_blank">gsil.engineering.uky.edu</a><br>
><br>
> On Mon, Dec 1, 2014 at 1:34 PM, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:<br>
> On Mon, Dec 1, 2014 at 12:33 PM, paul zhang <<a href="mailto:paulhuaizhang@gmail.com" target="_blank">paulhuaizhang@gmail.com</a>> wrote:<br>
> That is my new configuration. Is that OK?<br>
><br>
> export PETSC_DIR=`pwd`<br>
> export PETSC_ARCH=linux-gnu-intel<br>
> ./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack --download-mpich --with-valgrind-dir=/share/cluster/RHEL6.2/x86_64/apps/valgrind/3.9.0 --with-mpi=1 --with-mpi-dir=/home/hzh225/LIB_CFD/openmpi-1.8.3/<br>
><br>
> That looks correct.<br>
><br>
> When I say "using PETSc makefiles", I mean for your own project. You appear to be using CMake.<br>
><br>
> Matt<br>
><br>
><br>
> Huaibao (Paul) Zhang<br>
> Gas Surface Interactions Lab<br>
> Department of Mechanical Engineering<br>
> University of Kentucky,<br>
> Lexington,<br>
> KY, 40506-0503<br>
> Office: 216 Ralph G. Anderson Building<br>
> Web:<a href="http://gsil.engineering.uky.edu" target="_blank">gsil.engineering.uky.edu</a><br>
><br>
> On Mon, Dec 1, 2014 at 1:28 PM, paul zhang <<a href="mailto:paulhuaizhang@gmail.com" target="_blank">paulhuaizhang@gmail.com</a>> wrote:<br>
> I did use the PETSc makefiles. Should I include the valgrind path in my own make file again?<br>
><br>
> [hzh225@dlxlogin2-2 petsc-3.5.2]$ pwd<br>
> /home/hzh225/LIB_CFD/nP/petsc-3.5.2<br>
> [hzh225@dlxlogin2-2 petsc-3.5.2]$ make getincludedirs<br>
> -I/home/hzh225/LIB_CFD/nP/petsc-3.5.2/include -I/home/hzh225/LIB_CFD/nP/petsc-3.5.2/linux-gnu-intel/include -I/share/cluster/RHEL6.2/x86_64/apps/valgrind/3.9.0/include<br>
><br>
> Huaibao (Paul) Zhang<br>
> Gas Surface Interactions Lab<br>
> Department of Mechanical Engineering<br>
> University of Kentucky,<br>
> Lexington,<br>
> KY, 40506-0503<br>
> Office: 216 Ralph G. Anderson Building<br>
> Web:<a href="http://gsil.engineering.uky.edu" target="_blank">gsil.engineering.uky.edu</a><br>
><br>
> On Mon, Dec 1, 2014 at 11:55 AM, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:<br>
> On Mon, Dec 1, 2014 at 10:43 AM, paul zhang <<a href="mailto:paulhuaizhang@gmail.com" target="_blank">paulhuaizhang@gmail.com</a>> wrote:<br>
> Matt,<br>
><br>
> Thanks for your reply. I am able to compile PETSc. And I went through the default tests. Now when I go to my code, I got problems.<br>
><br>
> I am assuming that you put flags in your makefiles rather than using the PETSc makefiles. You need all the includes you get from<br>
><br>
> make getincludedirs<br>
><br>
> Matt<br>
><br>
> [hzh225@dlxlogin2-1 petsc-3.5]$ make all<br>
> [100%] Building CXX object CMakeFiles/kats.dir/main.cc.o<br>
> /home/hzh225/LIB_CFD/nP/petsc-3.5.2/include/petscsys.h(1760): catastrophic error: cannot open source file "valgrind/valgrind.h"<br>
> # include <valgrind/valgrind.h><br>
> ^<br>
><br>
> compilation aborted for /home/hzh225/CMake/petsc/petsc-3.5/main.cc (code 4)<br>
> make[2]: *** [CMakeFiles/kats.dir/main.cc.o] Error 4<br>
> make[1]: *** [CMakeFiles/kats.dir/all] Error 2<br>
> make: *** [all] Error 2<br>
><br>
><br>
> Huaibao (Paul) Zhang<br>
> Gas Surface Interactions Lab<br>
> Department of Mechanical Engineering<br>
> University of Kentucky,<br>
> Lexington,<br>
> KY, 40506-0503<br>
> Office: 216 Ralph G. Anderson Building<br>
> Web:<a href="http://gsil.engineering.uky.edu" target="_blank">gsil.engineering.uky.edu</a><br>
><br>
> On Mon, Dec 1, 2014 at 11:28 AM, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:<br>
> On Mon, Dec 1, 2014 at 10:21 AM, paul zhang <<a href="mailto:paulhuaizhang@gmail.com" target="_blank">paulhuaizhang@gmail.com</a>> wrote:<br>
> Hi All,<br>
><br>
> How to enable the valgrind flag? I installed that by myself locally.<br>
><br>
> It appears you do not have valgrind installed on your system. We HIGHLY recommend you install it from <a href="http://www.valgrind.org" target="_blank">www.valgrind.org</a> Or install valgrind-devel or equivalent using your package manager. Then rerun ./configure<br>
><br>
> We could not find the valgrind header (valgrind.h). You can use<br>
><br>
> --with-valgrind-dir=<path><br>
><br>
> so that it can find the path/include/valgrind/valgrind.h<br>
><br>
> Thanks,<br>
><br>
> Matt<br>
><br>
> Thanks,<br>
> Paul<br>
><br>
><br>
> Huaibao (Paul) Zhang<br>
><br>
><br>
><br>
><br>
> --<br>
> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
> -- Norbert Wiener<br>
><br>
><br>
><br>
><br>
> --<br>
> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
> -- Norbert Wiener<br>
><br>
><br>
><br>
><br>
><br>
> --<br>
> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
> -- Norbert Wiener<br>
><br>
<br>
</div></div></blockquote></div><br></div>
</blockquote></div></div></div><div><div class="h5"><br><br clear="all"><div><br></div>-- <br><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div>
</div></div></div></div>
</blockquote></div><br></div>