[mpich-discuss] [EXTERNAL] Re: Help Building MPICH 4.0b1: undefined references to hwloc

Wed Dec 15 09:44:34 CST 2021

Hi Matt,

Thanks for posting config.log.  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 hwloc.h while linking with external libhwloc.

We'll patch mpich to strengthen its config check. Meanwhile, you can pass --with-hwloc=embedded to the mpich configure to force both mpich and hydra to use embedded hwloc, which should bypass your issue.

Thanks for reporting!

--
Hui Zhou
________________________________
From: Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] <matthew.thompson at nasa.gov>
Sent: Wednesday, December 15, 2021 7:13 AM
To: discuss at mpich.org <discuss at mpich.org>
Cc: Zhou, Hui <zhouh at anl.gov>
Subject: Re: [EXTERNAL] Re: [mpich-discuss] Help Building MPICH 4.0b1: undefined references to hwloc

Hui,

Please find attached the requested config.log

Matt

--

Matt Thompson, SSAI, Ld Scientific Programmer/Analyst

NASA GSFC,    Global Modeling and Assimilation Office

Code 610.1,  8800 Greenbelt Rd,  Greenbelt,  MD 20771

Phone: 301-614-6712                 Fax: 301-614-6246

http://science.gsfc.nasa.gov/sed/bio/matthew.thompson

From: "Zhou, Hui via discuss" <discuss at mpich.org>
Reply-To: "discuss at mpich.org" <discuss at mpich.org>
Date: Tuesday, December 14, 2021 at 6:14 PM
To: "discuss at mpich.org" <discuss at mpich.org>
Cc: "Zhou, Hui" <zhouh at anl.gov>
Subject: [EXTERNAL] Re: [mpich-discuss] Help Building MPICH 4.0b1: undefined references to hwloc

Hi Matt,

Could post your src/pm/hydra/config.log?

--

Hui Zhou

________________________________

From: Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] via discuss <discuss at mpich.org>
Sent: Tuesday, December 14, 2021 2:40 PM
To: discuss at mpich.org <discuss at mpich.org>
Cc: Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] <matthew.thompson at nasa.gov>
Subject: [mpich-discuss] Help Building MPICH 4.0b1: undefined references to hwloc

MPICH Discuss,

I'm sure I've done something stupid, but I'm not sure what. I tried searching google, but my google-fu failed me.

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:

./configure CC=gcc CXX=g++ FC=gfortran \

  FCFLAGS=-fallow-argument-mismatch \

  FFLAGS=-fallow-argument-mismatch \

  --prefix=/discover/swdev/gmao_SIteam/MPI/mpich/4.0b1/gcc-11.2.0

The MPICH configure step was nice enough to let me know I needed those FFLAGS and FCFLAGS. And it configured just happily.[1]

When I went to the make step I eventually it errored out with:

make[3]: Entering directory '/gpfsm/dswdev/gmao_SIteam/MPI/src/mpich-4.0b1/src/pm/hydra'

  CCLD     libpm.la

  CCLD     hydra_persist

/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':

/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'

collect2: error: ld returned 1 exit status

Makefile:1286: recipe for target 'hydra_persist' failed

make[3]: *** [hydra_persist] Error 1

Now, as far as I can tell from the configure output, I'm using the embedded hwloc:

checking if hwloc meets minimum version requirement... no

configure: ===== configuring modules/hwloc =====

...

### Configuring hwloc core

###

checking hwloc building mode... embedded

configure: hwloc builddir: /discover/swdev/gmao_SIteam/MPI/src/mpich-4.0b1/modules/hwloc

configure: hwloc srcdir: /discover/swdev/gmao_SIteam/MPI/src/mpich-4.0b1/modules/hwloc

...

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).

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.

Thanks for any help,

Matt

[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?

--

Matt Thompson, SSAI, Ld Scientific Programmer/Analyst

NASA GSFC,    Global Modeling and Assimilation Office

Code 610.1,  8800 Greenbelt Rd,  Greenbelt,  MD 20771

Phone: 301-614-6712                 Fax: 301-614-6246

http://science.gsfc.nasa.gov/sed/bio/matthew.thompson
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