<div dir="ltr">Thanks, Glad to know you have a workaround.<br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">--Junchao Zhang</div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Apr 10, 2021 at 10:06 PM Danyang Su <<a href="mailto:danyang.su@gmail.com">danyang.su@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div lang="EN-CA" style="overflow-wrap: break-word;"><div class="gmail-m_5270362316078900786WordSection1"><p class="MsoNormal">Hi Junchao,<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">I cannot configure your branch with same options due to the error in sowing. I had similar error before on other clusters with very old openmpi version. Problem was solved when openmpi was updated to a newer one. <u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">At this moment, I configured a PETSc version with Openmpi 2.1.6 version and it seems working properly. <u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Thanks and have a good rest of the weekend,<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Danyang<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(181,196,223);padding:3pt 0cm 0cm"><p class="MsoNormal"><b><span style="font-size:12pt;color:black">From: </span></b><span style="font-size:12pt;color:black">Danyang Su <<a href="mailto:danyang.su@gmail.com" target="_blank">danyang.su@gmail.com</a>><br><b>Date: </b>Saturday, April 10, 2021 at 4:08 PM<br><b>To: </b>Junchao Zhang <<a href="mailto:junchao.zhang@gmail.com" target="_blank">junchao.zhang@gmail.com</a>><br><b>Cc: </b>Barry Smith <<a href="mailto:bsmith@petsc.dev" target="_blank">bsmith@petsc.dev</a>>, "<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>" <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>><br><b>Subject: </b>Re: [petsc-users] Undefined reference in PETSc 3.13+ with old MPI version<u></u><u></u></span></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><p class="MsoNormal">Hi Junchao,<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">The configuration is successful. The error comes from the last step when I run <u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="gmail-m_5270362316078900786p1"><span class="gmail-m_5270362316078900786s1">make PETSC_DIR=/home/danyangs/soft/petsc/petsc-3.13.6 PETSC_ARCH=linux-intel-openmpi check</span><u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal"><b><span style="font-size:8.5pt;font-family:Menlo;color:rgb(202,51,35)">*******************Error detected during compile or link!*******************</span></b><u></u><u></u></p><p class="MsoNormal"><b><span style="font-size:8.5pt;font-family:Menlo;color:rgb(202,51,35)">See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html</a></span></b><u></u><u></u></p><p class="MsoNormal"><b><span style="font-size:8.5pt;font-family:Menlo;color:rgb(202,51,35)">/home/danyangs/soft/petsc/petsc-3.13.6/src/snes/tutorials ex5f</span></b><u></u><u></u></p><p class="MsoNormal"><b><span style="font-size:8.5pt;font-family:Menlo;color:rgb(202,51,35)">*********************************************************</span></b><u></u><u></u></p><p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">mpif90 -fPIC -O3 -march=native -mtune=nativels -I/home/danyangs/soft/petsc/petsc-3.13.6/include -I/home/danyangs/soft/petsc/petsc-3.13.6/linux-intel-openmpi/include ex5f.F90 -Wl,-rpath,/home/danyangs/soft/petsc/petsc-3.13.6/linux-intel-openmpi/lib -L/home/danyangs/soft/petsc/petsc-3.13.6/linux-intel-openmpi/lib -Wl,-rpath,/home/danyangs/soft/petsc/petsc-3.13.6/linux-intel-openmpi/lib -L/home/danyangs/soft/petsc/petsc-3.13.6/linux-intel-openmpi/lib -Wl,-rpath,/global/software/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64 -L/global/software/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64 -Wl,-rpath,/global/software/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64 -L/global/software/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64 -Wl,-rpath,/global/software/openmpi-1.6.5/intel/lib64 -L/global/software/openmpi-1.6.5/intel/lib64 -Wl,-rpath,/global/software/intel/composerxe/mkl/lib/intel64 -L/global/software/intel/composerxe/mkl/lib/intel64 -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -Wl,-rpath,/global/software/intel/composerxe/lib/intel64 -lpetsc -lHYPRE -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lsuperlu -lflapack -lfblas -lX11 -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lparmetis -lmetis -lstdc++ -ldl -lmpi_f90 -lmpi_f77 -lmpi -lm -lnuma -lrt -lnsl -lutil -limf -lifport -lifcore -lsvml -lipgo -lintlc -lpthread -lgcc_s -lirc_s -lstdc++ -ldl -o ex5f</span><u></u><u></u></p><p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">ifort: command line warning #10159: invalid argument for option '-m'</span><u></u><u></u></p><p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">/home/danyangs/soft/petsc/petsc-3.13.6/linux-intel-openmpi/lib/libpetsc.so: undefined reference to `MPI_Win_allocate'</span><u></u><u></u></p><p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">/home/danyangs/soft/petsc/petsc-3.13.6/linux-intel-openmpi/lib/libpetsc.so: undefined reference to `MPI_Win_attach'</span><u></u><u></u></p><p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">/home/danyangs/soft/petsc/petsc-3.13.6/linux-intel-openmpi/lib/libpetsc.so: undefined reference to `MPI_Win_create_dynamic'</span><u></u><u></u></p><p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">gmake[4]: *** [ex5f] Error 1</span><u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">Thanks,<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">Danyang<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(181,196,223);padding:3pt 0cm 0cm"><p class="MsoNormal"><b><span style="font-size:12pt;color:black">From: </span></b><span style="font-size:12pt;color:black">Junchao Zhang <<a href="mailto:junchao.zhang@gmail.com" target="_blank">junchao.zhang@gmail.com</a>><br><b>Date: </b>Saturday, April 10, 2021 at 3:57 PM<br><b>To: </b>Danyang Su <<a href="mailto:danyang.su@gmail.com" target="_blank">danyang.su@gmail.com</a>><br><b>Cc: </b>Barry Smith <<a href="mailto:bsmith@petsc.dev" target="_blank">bsmith@petsc.dev</a>>, "<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>" <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>><br><b>Subject: </b>Re: [petsc-users] Undefined reference in PETSc 3.13+ with old MPI version</span><u></u><u></u></p></div><div><p class="MsoNormal"> <u></u><u></u></p></div><div><p class="MsoNormal">You sent a wrong one. This configure.log was from a successful configuration. Note <span style="font-size:8.5pt;font-family:Menlo;color:black">FOPTFLAGS="-O3 -march=native -mtune=</span><span style="font-size:8.5pt;font-family:Menlo;color:red">nativels</span><span style="font-size:8.5pt;font-family:Menlo;color:black">" </span>looks suspicious.<u></u><u></u></p><div><p class="MsoNormal"> <u></u><u></u></p></div><div><div><div><div><p class="MsoNormal">--Junchao Zhang<u></u><u></u></p></div></div></div><p class="MsoNormal"> <u></u><u></u></p></div></div><p class="MsoNormal"> <u></u><u></u></p><div><div><p class="MsoNormal">On Sat, Apr 10, 2021 at 5:32 PM Danyang Su <<a href="mailto:danyang.su@gmail.com" target="_blank">danyang.su@gmail.com</a>> wrote:<u></u><u></u></p></div><blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0cm 0cm 0cm 6pt;margin:5pt 0cm 5pt 4.8pt"><div><div><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">Hi Junchao,<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">Thanks for looking into this problem. The configuration log is attached.<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">All the best,<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">Danyang<u></u><u></u></p><div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(181,196,223);padding:3pt 0cm 0cm"><p class="MsoNormal"><b><span style="font-size:12pt;color:black">From: </span></b><span style="font-size:12pt;color:black">Junchao Zhang <<a href="mailto:junchao.zhang@gmail.com" target="_blank">junchao.zhang@gmail.com</a>><br><b>Date: </b>Saturday, April 10, 2021 at 2:36 PM<br><b>To: </b>Danyang Su <<a href="mailto:danyang.su@gmail.com" target="_blank">danyang.su@gmail.com</a>><br><b>Cc: </b>Barry Smith <<a href="mailto:bsmith@petsc.dev" target="_blank">bsmith@petsc.dev</a>>, "<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>" <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>><br><b>Subject: </b>Re: [petsc-users] Undefined reference in PETSc 3.13+ with old MPI version</span><u></u><u></u></p></div><div><p class="MsoNormal"> <u></u><u></u></p></div><div><div><p class="MsoNormal">Hi, Danyang, <u></u><u></u></p></div><div><p class="MsoNormal"> <u></u><u></u></p></div><p class="MsoNormal">Send the configure.log. Also, PETSc does not need MPI_Win_allocate etc to work. I will have a look.<u></u><u></u></p><div><p class="MsoNormal"><br clear="all"><u></u><u></u></p><div><div><div><p class="MsoNormal">--Junchao Zhang<u></u><u></u></p></div></div></div><p class="MsoNormal"> <u></u><u></u></p></div></div><p class="MsoNormal"> <u></u><u></u></p><div><div><p class="MsoNormal">On Sat, Apr 10, 2021 at 2:47 PM Danyang Su <<a href="mailto:danyang.su@gmail.com" target="_blank">danyang.su@gmail.com</a>> wrote:<u></u><u></u></p></div><blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0cm 0cm 0cm 6pt;margin:5pt 0cm 5pt 4.8pt"><div><div><p class="MsoNormal">Hi Barry,<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">I tried this option before but get ‘Error running configure on OpenMPI’<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">*******************************************************************************</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">UNABLE to CONFIGURE with GIVEN OPTIONS</span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">(see configure.log for details):</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">-------------------------------------------------------------------------------</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">Error running configure on OPENMPI</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">*******************************************************************************</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/configure.py", line 456, in petsc_configure</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">framework.configure(out = sys.stdout)</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/framework.py", line 1253, in configure</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">self.processChildren()</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/framework.py", line 1242, in processChildren</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">self.serialEvaluation(self.childGraph)</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/framework.py", line 1217, in serialEvaluation</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">child.configure()</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/package.py", line 1144, in configure</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">self.executeTest(self.configureLibrary)</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/base.py", line 140, in executeTest</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">ret = test(*args,**kargs)</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/package.py", line 902, in configureLibrary</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">for location, directory, lib, incl in self.generateGuesses():</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/package.py", line 476, in generateGuesses</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">d = self.checkDownload()</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/packages/OpenMPI.py", line 56, in checkDownload</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">return self.getInstallDir()</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/package.py", line 365, in getInstallDir</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">installDir = self.Install()</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/packages/OpenMPI.py", line 63, in Install</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">installDir = config.package.GNUPackage.Install(self)</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/package.py", line 1667, in Install</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space"> </span><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">raise RuntimeError('Error running configure on ' + self.PACKAGE)</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">================================================================================</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">Finishing configure run at Sat, 10 Apr 2021 11:57:20 -0700</span><u></u><u></u></p><p class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262p1"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1">================================================================================</span><u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">Thanks,<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">Danyang<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(181,196,223);padding:3pt 0cm 0cm"><p class="MsoNormal"><b><span style="font-size:12pt;color:black">From: </span></b><span style="font-size:12pt;color:black">Barry Smith <<a href="mailto:bsmith@petsc.dev" target="_blank">bsmith@petsc.dev</a>><br><b>Date: </b>Saturday, April 10, 2021 at 10:31 AM<br><b>To: </b>Danyang Su <<a href="mailto:danyang.su@gmail.com" target="_blank">danyang.su@gmail.com</a>><br><b>Cc: </b>"<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>" <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>><br><b>Subject: </b>Re: [petsc-users] Undefined reference in PETSc 3.13+ with old MPI version</span><u></u><u></u></p></div><div><p class="MsoNormal"> <u></u><u></u></p></div><div><p class="MsoNormal"> <u></u><u></u></p></div><p class="MsoNormal"> Depending on the network you can remove the ./configure options --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 and use instead --with-cc=icc --with-cxx=icpc and--with-fc=ifort --download-openmpi <u></u><u></u></p><div><p class="MsoNormal"> <u></u><u></u></p></div><div><p class="MsoNormal"> Barry<u></u><u></u></p></div><div><p class="MsoNormal"> <u></u><u></u></p><div><p class="MsoNormal" style="margin-bottom:12pt"> <u></u><u></u></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><div><p class="MsoNormal">On Apr 10, 2021, at 12:18 PM, Danyang Su <<a href="mailto:danyang.su@gmail.com" target="_blank">danyang.su@gmail.com</a>> wrote:<u></u><u></u></p></div><p class="MsoNormal"> <u></u><u></u></p><div><div><p class="MsoNormal"><span lang="EN-US">Dear PETSc developers and users,</span><u></u><u></u></p></div><div><p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p></div><div><p class="MsoNormal"><span lang="EN-US">I am trying to install the latest PETSc version on an ancient cluster. The OpenMPI version is 1.6.5 and Compiler is Intel 14.0, which are the newest on that cluster. I have no problem to install PETSc up to version 3.12.5. However, if I try to use PETSc 3.13+, there are three undefined reference errors in MPI_Win_allocate, MPI_Win_attach and MPI_Win_create_dynamic. I know these three functions are available from OpenMPI 2.0+. Because the cluster is not in technical support anymore, there is no way I can install new OpenMPI version or do some update. Is it possible to disable these three functions in PETSc 3.13+ version?</span><u></u><u></u></p></div><div><p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p></div><div><p class="MsoNormal"><span lang="EN-US">The errors occur in ‘make check’ step:</span><u></u><u></u></p></div><div><p class="MsoNormal"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1"><span style="font-size:8.5pt;font-family:Menlo">/home/dsu/soft/petsc/petsc-3.13.0/linux-intel-openmpi/lib/libpetsc.so: undefined reference to `MPI_Win_allocate'</span></span><u></u><u></u></p></div><div><p class="MsoNormal"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1"><span style="font-size:8.5pt;font-family:Menlo">/home/dsu/soft/petsc/petsc-3.13.0/linux-intel-openmpi/lib/libpetsc.so: undefined reference to `MPI_Win_attach'</span></span><u></u><u></u></p></div><div><p class="MsoNormal"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1"><span style="font-size:8.5pt;font-family:Menlo">/home/dsu/soft/petsc/petsc-3.13.0/linux-intel-openmpi/lib/libpetsc.so: undefined reference to `MPI_Win_create_dynamic'</span></span><u></u><u></u></p></div><div><p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p></div><div><p class="MsoNormal"><span lang="EN-US">The configuration used is shown below:</span><u></u><u></u></p></div><div><p class="MsoNormal"><span class="gmail-m_5270362316078900786gmail-m703022312349564466gmail-m2680357209072920262s1"><span style="font-size:8.5pt;font-family:Menlo">./configure --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-mumps --download-scalapack --download-parmetis --download-metis --download-fblaslapack --download-hypre --download-superlu --download-hdf5=yes --with-debugging=0 COPTFLAGS="-O3 -march=native -mtune=native" CXXOPTFLAGS="-O3 -march=native -mtune=native" FOPTFLAGS="-O3 -march=native -mtune=nativels"</span></span><u></u><u></u></p></div><div><p class="MsoNormal"> <u></u><u></u></p></div><div><p class="MsoNormal">Thanks,<u></u><u></u></p></div><div><p class="MsoNormal"> <u></u><u></u></p></div><div><p class="MsoNormal">Danyang<u></u><u></u></p></div></div></blockquote></div><p class="MsoNormal"> <u></u><u></u></p></div></div></div></blockquote></div></div></div></blockquote></div></div></div>
</blockquote></div>