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--></style></head><body lang=EN-CA link=blue vlink=purple style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal>Hi Junchao,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></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. <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>At this moment, I configured a PETSc version with Openmpi 2.1.6 version and it seems working properly. <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thanks and have a good rest of the weekend,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Danyang<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span style='font-size:12.0pt;color:black'>From: </span></b><span style='font-size:12.0pt;color:black'>Danyang Su <danyang.su@gmail.com><br><b>Date: </b>Saturday, April 10, 2021 at 4:08 PM<br><b>To: </b>Junchao Zhang <junchao.zhang@gmail.com><br><b>Cc: </b>Barry Smith <bsmith@petsc.dev>, "petsc-users@mcs.anl.gov" <petsc-users@mcs.anl.gov><br><b>Subject: </b>Re: [petsc-users] Undefined reference in PETSc 3.13+ with old MPI version<o:p></o:p></span></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>Hi Junchao,<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>The configuration is successful. The error comes from the last step when I run <o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=p1><span class=s1>make PETSC_DIR=/home/danyangs/soft/petsc/petsc-3.13.6 PETSC_ARCH=linux-intel-openmpi check</span><o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal><b><span style='font-size:8.5pt;font-family:Menlo;color:#CA3323'>*******************Error detected during compile or link!*******************</span></b><o:p></o:p></p><p class=MsoNormal><b><span style='font-size:8.5pt;font-family:Menlo;color:#CA3323'>See http://www.mcs.anl.gov/petsc/documentation/faq.html</span></b><o:p></o:p></p><p class=MsoNormal><b><span style='font-size:8.5pt;font-family:Menlo;color:#CA3323'>/home/danyangs/soft/petsc/petsc-3.13.6/src/snes/tutorials ex5f</span></b><o:p></o:p></p><p class=MsoNormal><b><span style='font-size:8.5pt;font-family:Menlo;color:#CA3323'>*********************************************************</span></b><o:p></o:p></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><o:p></o:p></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><o:p></o:p></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><o:p></o:p></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><o:p></o:p></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><o:p></o:p></p><p class=MsoNormal><span style='font-size:8.5pt;font-family:Menlo;color:black'>gmake[4]: *** [ex5f] Error 1</span><o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>Thanks,<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>Danyang<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span style='font-size:12.0pt;color:black'>From: </span></b><span style='font-size:12.0pt;color:black'>Junchao Zhang <junchao.zhang@gmail.com><br><b>Date: </b>Saturday, April 10, 2021 at 3:57 PM<br><b>To: </b>Danyang Su <danyang.su@gmail.com><br><b>Cc: </b>Barry Smith <bsmith@petsc.dev>, "petsc-users@mcs.anl.gov" <petsc-users@mcs.anl.gov><br><b>Subject: </b>Re: [petsc-users] Undefined reference in PETSc 3.13+ with old MPI version</span><o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></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.<o:p></o:p></p><div><p class=MsoNormal> <o:p></o:p></p></div><div><div><div><div><p class=MsoNormal>--Junchao Zhang<o:p></o:p></p></div></div></div><p class=MsoNormal> <o:p></o:p></p></div></div><p class=MsoNormal> <o:p></o:p></p><div><div><p class=MsoNormal>On Sat, Apr 10, 2021 at 5:32 PM Danyang Su <<a href="mailto:danyang.su@gmail.com">danyang.su@gmail.com</a>> wrote:<o:p></o:p></p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt'><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hi Junchao,<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Thanks for looking into this problem. The configuration log is attached.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>All the best,<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Danyang<o:p></o:p></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span style='font-size:12.0pt;color:black'>From: </span></b><span style='font-size:12.0pt;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><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hi, Danyang, <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Send the configure.log. Also, PETSc does not need MPI_Win_allocate etc to work. I will have a look.<o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><br clear=all><o:p></o:p></p><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>--Junchao Zhang<o:p></o:p></p></div></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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:<o:p></o:p></p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt'><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hi Barry,<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I tried this option before but get ‘Error running configure on OpenMPI’<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>*******************************************************************************</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>UNABLE to CONFIGURE with GIVEN OPTIONS</span><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>(see configure.log for details):</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>-------------------------------------------------------------------------------</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>Error running configure on OPENMPI</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>*******************************************************************************</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/configure.py", line 456, in petsc_configure</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>framework.configure(out = sys.stdout)</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/framework.py", line 1253, in configure</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>self.processChildren()</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/framework.py", line 1242, in processChildren</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>self.serialEvaluation(self.childGraph)</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/framework.py", line 1217, in serialEvaluation</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>child.configure()</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/package.py", line 1144, in configure</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>self.executeTest(self.configureLibrary)</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/base.py", line 140, in executeTest</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>ret = test(*args,**kargs)</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/package.py", line 902, in configureLibrary</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>for location, directory, lib, incl in self.generateGuesses():</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/package.py", line 476, in generateGuesses</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>d = self.checkDownload()</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/packages/OpenMPI.py", line 56, in checkDownload</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>return self.getInstallDir()</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/package.py", line 365, in getInstallDir</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>installDir = self.Install()</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/packages/OpenMPI.py", line 63, in Install</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>installDir = config.package.GNUPackage.Install(self)</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>File "/global/home/danyangs/soft/petsc/petsc-3.14.6/config/BuildSystem/config/package.py", line 1667, in Install</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262apple-converted-space> </span><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>raise RuntimeError('Error running configure on ' + self.PACKAGE)</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>================================================================================</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>Finishing configure run at Sat, 10 Apr 2021 11:57:20 -0700</span><o:p></o:p></p><p class=gmail-m703022312349564466gmail-m2680357209072920262p1><span class=gmail-m703022312349564466gmail-m2680357209072920262s1>================================================================================</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Thanks,<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Danyang<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span style='font-size:12.0pt;color:black'>From: </span></b><span style='font-size:12.0pt;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><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> 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 <o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> Barry<o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'> <o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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:<o:p></o:p></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US>Dear PETSc developers and users,</span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> </span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> </span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US>The errors occur in ‘make check’ step:</span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span class=gmail-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><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span class=gmail-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><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span class=gmail-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><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> </span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US>The configuration used is shown below:</span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span class=gmail-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><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Thanks,<o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Danyang<o:p></o:p></p></div></div></blockquote></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div></blockquote></div></div></div></blockquote></div></div></body></html>