<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">You don’t need to set environment variables CC, FC, CXX, CPPFLAGS, or LDFLAGS.<div class="">Could you try the following command and let me know?</div><div class=""><br class=""><div class="">MPIF77=mpiifort MPIF90=mpiifort MPICC=mpiicc MPICXX=mpiicpc ./configure --prefix=/mnt/nfs/home/b4064989/library/netcdf-parallel/intel/1.9.0 --enable-shared</div><div class=""><br class=""><div class="">
Wei-keng
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<div><br class=""><blockquote type="cite" class=""><div class="">On May 8, 2018, at 2:44 PM, Estanislao Gavilan Pascual-Ahuir (PGR) <<a href="mailto:E.Gavilan-Pascual-Ahuir1@newcastle.ac.uk" class="">E.Gavilan-Pascual-Ahuir1@newcastle.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi Robb,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I think you were right. It seems openmpi is linked with munge. So I decided to use intel compilers intead of GNU. The building works quite smoothly until it reaches the ncmpigen where it says that :</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div class="">./../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_cpystr'<br class="">../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_allocate'<br class="">../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_dealloc_allocatable'<br class="">../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_cpstr'<br class="">../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_alloc_allocatable'<br class="">../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_len_trim'<br class="">../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_array_copy_in'<br class="">../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_trim'<br class="">../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_contig_array'<br class="">../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_check_mult_overflow64'<br class="">../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_array_copy_out'<br class=""></div><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I think these function are related to the fortran libraries. However, I am not sure how to add the library path in the ./configuration line. This is the configuration that I am setting</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div class="">MPIF77=mpiifort MPIF90=mpiifort MPICC=mpiicc MPICXX=mpiicpc CC=mpiicc FC=mpiifort CXX=mpiicpc CPPFLAGS="-I/mnt/nfs/home/b4064989/library/zlib/intel/1.2.11/include -I/mnt/nfs/home/b4064989/library/hdf5/intel/1.10.2/include" LDFLAGS="-L/mnt/nfs/home/b4064989/library/zlib/intel/1.2.11/lib -L/mnt/nfs/home/b4064989/library/hdf5/intel/1.10.2/lib" ./configure --prefix=/mnt/nfs/home/b4064989/library/netcdf-parallel/intel/1.9.0 --enable-shared</div><div class=""><br class=""></div><div class="">Am I missing something? Thanks so much for your help.<span class="Apple-converted-space"> </span></div><div class=""><br class=""></div><div class="">Estanis<br class=""></div><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div></div><hr tabindex="-1" style="font-family: Monaco; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; display: inline-block; width: 643.859375px;" class=""><span style="font-family: Monaco; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""></span><div id="divRplyFwdMsg" dir="ltr" style="font-family: Monaco; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Latham, Robert J. <<a href="mailto:robl@mcs.anl.gov" class="">robl@mcs.anl.gov</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>07 May 2018 19:53:53<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:parallel-netcdf@mcs.anl.gov" class="">parallel-netcdf@mcs.anl.gov</a>; Estanislao Gavilan Pascual-Ahuir (PGR)<br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: error building pnetcdf</font><div class=""> </div></div><div class="BodyFragment" style="font-family: Monaco; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><font size="2" class=""><span style="font-size: 11pt;" class=""><div class="PlainText">On Mon, 2018-05-07 at 14:13 +0000, Estanislao Gavilan Pascual-Ahuir<br class="">(PGR) wrote:<br class="">> Good afternoon,<br class="">><span class="Apple-converted-space"> </span><br class="">> I am trying to build the pnetcdf with shared enable. I am having this<br class="">> error (attach picture). Do I need the libmunge for pnetcdf? I have<br class="">> even tried to add the path to libmunge (/lib64) but I<br class="">> cannot solve the problem. Am I missing something? Thanks in advance<br class="">> for your help.<br class=""><br class="">I don't know where 'libmunge' came from. That's not part of parallel-<br class="">netcdf. Can you double-check your environment and figure out what<br class="">wants to use that library?<br class=""><br class="">==rob</div></span></font></div></div></blockquote></div><br class=""></div></div></body></html>