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Hi Matt,</div>
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Thanks for posting <code>config.log</code>. I found the issue. Both mpich the library and hydra the program uses hwloc and independently tries to probe hwloc. Because hydra is configured as a subdir inside mpich configure, it inherits the CFLAGS from mpich,
resulting in using embedded <code>hwloc.h</code> while linking with external <code>
libhwloc</code>.</div>
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We'll patch mpich to strengthen its config check. Meanwhile, you can pass <code>--with-hwloc=embedded</code> to the mpich configure to force both mpich and hydra to use embedded hwloc, which should bypass your issue. <br>
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Thanks for reporting!</div>
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-- <br>
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Hui Zhou<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] <matthew.thompson@nasa.gov><br>
<b>Sent:</b> Wednesday, December 15, 2021 7:13 AM<br>
<b>To:</b> discuss@mpich.org <discuss@mpich.org><br>
<b>Cc:</b> Zhou, Hui <zhouh@anl.gov><br>
<b>Subject:</b> Re: [EXTERNAL] Re: [mpich-discuss] Help Building MPICH 4.0b1: undefined references to hwloc</font>
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<p class="x_MsoNormal"><span style="font-size:12.0pt; font-family:Consolas">Hui,</span></p>
<p class="x_MsoNormal"><span style="font-size:12.0pt; font-family:Consolas"> </span></p>
<p class="x_MsoNormal"><span style="font-size:12.0pt; font-family:Consolas">Please find attached the requested config.log</span></p>
<p class="x_MsoNormal"><span style="font-size:12.0pt; font-family:Consolas"> </span></p>
<p class="x_MsoNormal"><span style="font-size:12.0pt; font-family:Consolas">Matt</span></p>
<p class="x_MsoNormal"><span style="font-size:12.0pt; font-family:Consolas"> </span></p>
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<p class="x_MsoNormal"><span style="font-size:12.0pt; font-family:Consolas">-- </span></p>
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<p class="x_MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt; font-family:Consolas">Matt Thompson, SSAI, Ld Scientific Programmer/Analyst</span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt; font-family:Consolas">NASA GSFC, Global Modeling and Assimilation Office</span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt; font-family:Consolas">Code 610.1, 8800 Greenbelt Rd, Greenbelt, MD 20771</span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt; font-family:Consolas">Phone: 301-614-6712 Fax: 301-614-6246</span></p>
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<p class="x_MsoNormal"><u><span style="font-size:12.0pt; font-family:Consolas; color:#0000E9">http://science.gsfc.nasa.gov/sed/bio/matthew.thompson</span></u><span style="font-size:12.0pt; font-family:Consolas"></span></p>
<p class="x_MsoNormal"><span style="font-size:12.0pt; font-family:Consolas"> </span></p>
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<p class="x_MsoNormal"><b><span style="font-size:12.0pt; color:black">From: </span>
</b><span style="font-size:12.0pt; color:black">"Zhou, Hui via discuss" <discuss@mpich.org><br>
<b>Reply-To: </b>"discuss@mpich.org" <discuss@mpich.org><br>
<b>Date: </b>Tuesday, December 14, 2021 at 6:14 PM<br>
<b>To: </b>"discuss@mpich.org" <discuss@mpich.org><br>
<b>Cc: </b>"Zhou, Hui" <zhouh@anl.gov><br>
<b>Subject: </b>[EXTERNAL] Re: [mpich-discuss] Help Building MPICH 4.0b1: undefined references to hwloc</span></p>
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<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black">Hi Matt,</span></p>
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<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black"> </span></p>
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<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black">Could post your
</span><code><span style="font-size:10.0pt; color:black">src/pm/hydra/config.log</span></code><span style="font-size:12.0pt; color:black">?</span></p>
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<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black"> </span></p>
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<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black">-- </span></p>
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<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black">Hui Zhou</span></p>
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<p class="x_MsoNormal"><b><span style="color:black">From:</span></b><span style="color:black"> Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] via discuss <discuss@mpich.org><br>
<b>Sent:</b> Tuesday, December 14, 2021 2:40 PM<br>
<b>To:</b> discuss@mpich.org <discuss@mpich.org><br>
<b>Cc:</b> Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] <matthew.thompson@nasa.gov><br>
<b>Subject:</b> [mpich-discuss] Help Building MPICH 4.0b1: undefined references to hwloc</span>
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<p class="x_xmsonormal"><span style="font-family:Consolas">MPICH Discuss,</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> </span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">I'm sure I've done something stupid, but I'm not sure what. I tried searching google, but my google-fu failed me.
</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> </span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">Today I decided to try and build MPICH 4.0b1 on a cluster I'm on (NCCS Discover) using GCC 11.2. My configure line was quite boring:</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> </span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">./configure CC=gcc CXX=g++ FC=gfortran \</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> FCFLAGS=-fallow-argument-mismatch \</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> FFLAGS=-fallow-argument-mismatch \</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> --prefix=/discover/swdev/gmao_SIteam/MPI/mpich/4.0b1/gcc-11.2.0
</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> </span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">The MPICH configure step was nice enough to let me know I needed those FFLAGS and FCFLAGS. And it configured just happily.[1]</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> </span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">When I went to the make step I eventually it errored out with:</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> </span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">make[3]: Entering directory '/gpfsm/dswdev/gmao_SIteam/MPI/src/mpich-4.0b1/src/pm/hydra'</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> CCLD libpm.la</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> CCLD hydra_persist</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">/usr/bin/ld: /discover/swdev/gmao_SIteam/MPI/src/mpich-4.0b1/src/pm/hydra/.libs/libhydra.a(topo_hwloc.o): in function `HYDT_topo_hwloc_init':</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">/discover/swdev/gmao_SIteam/MPI/src/mpich-4.0b1/src/pm/hydra/tools/topo/hwloc/topo_hwloc.c:577: undefined reference to `hwloc_topology_set_io_types_filter'</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">collect2: error: ld returned 1 exit status</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">Makefile:1286: recipe for target 'hydra_persist' failed</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">make[3]: *** [hydra_persist] Error 1</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> </span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">Now, as far as I can tell from the configure output, I'm using the embedded hwloc:</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> </span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">checking if hwloc meets minimum version requirement... no</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">configure: ===== configuring modules/hwloc =====</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">...</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">### Configuring hwloc core</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">###</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">checking hwloc building mode... embedded</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">configure: hwloc builddir: /discover/swdev/gmao_SIteam/MPI/src/mpich-4.0b1/modules/hwloc</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">configure: hwloc srcdir: /discover/swdev/gmao_SIteam/MPI/src/mpich-4.0b1/modules/hwloc</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">...</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> </span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">And I can't see anything in the output that it's somehow picking up on an hwloc I might have installed somewhere else (be it Open MPI or just hwloc by hand).</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> </span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">Maybe there are flags I need to pass? I do see reference to --with-hwloc=embedded, but it looks like configure decided to use that itself.
</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> </span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">Thanks for any help,</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">Matt</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> </span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> </span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">[1] Note: I'm building on an Infiniband system so maybe I need to do a build with --with-device=ch4:ucx eventually, but that's a runtime thing. I figure it can't be involved with this error...right?</span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas"> </span></p>
<p class="x_xmsonormal"><span style="font-family:Consolas">-- </span></p>
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<p class="x_xmsonormal" style="text-autospace:none"><span style="font-family:Consolas">Matt Thompson, SSAI, Ld Scientific Programmer/Analyst</span></p>
<p class="x_xmsonormal" style="text-autospace:none"><span style="font-family:Consolas">NASA GSFC, Global Modeling and Assimilation Office</span></p>
<p class="x_xmsonormal" style="text-autospace:none"><span style="font-family:Consolas">Code 610.1, 8800 Greenbelt Rd, Greenbelt, MD 20771</span></p>
<p class="x_xmsonormal" style="text-autospace:none"><span style="font-family:Consolas">Phone: 301-614-6712 Fax: 301-614-6246</span></p>
</div>
<p class="x_xmsonormal"><u><span style="font-family:Consolas; color:#0000E9">http://science.gsfc.nasa.gov/sed/bio/matthew.thompson</span></u></p>
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