helpManeage - Support: sr #110370, OpenMPI fails on macOS

 
 

sr #110370: OpenMPI fails on macOS

Submitted by:  None
Submitted on:  Wed 11 Nov 2020 10:43:28 AM UTC  
 
Category:  None Priority:  5 - Normal
Severity:  4 - Important Status:  None
Privacy:  Public Assigned to:  None
Originator Email:  -email is unavailable- Open/Closed:  Open
Operating System:  Mac OS

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( Jump to the original submission)

Mon 16 Nov 2020 12:10:00 PM UTC, comment #7: 

Thanks, but I couldn't find any commit with the 'c853b2c' hash in the Maneage branch. Can you point us to the Git repository of the project you are building?

If you add 'maneage' to the end of the 'git describe' command, it will print the last commit in the 'maneage' branch (that is shared in all projects) and we won't have to worry about the specific project (especially since this is a low-level issue that is rarely modified in "Maneaged" projects).

 git describe --always maneage

Mohammad Akhlaghi <makhlaghi>
Project Administrator
Mon 16 Nov 2020 09:54:52 AM UTC, comment #6: 

git describe --always --long --dirty
c853b2c

Ana M Perez <anampgajate>
Thu 12 Nov 2020 06:40:51 PM UTC, comment #5: 

This look like scipy-1.3.1:

    41  cd /BUILD/build-tmp; rm -rf  scipy-1.3.1; if !  tar xf /BUILD/tarballs/scipy-1.3.1.tar.gz; then echo; echo "Tar error"; exit 1; fi; cd  scipy-1.3.1; if [ "x$conf" != x ]; then sed -e 's|@LIBDIR[@]|'"/BUILD/installed/lib"'|' -e 's|@INCDIR[@]|'"/BUILD/installed/include"'|' $conf > site.cfg; fi; if type pyhook_before &>/dev/null; then pyhook_before; fi && python setup.py build && python setup.py install && if type pyhook_after &>/dev/null; then pyhook_after; fi && cd .. && rm -rf  scipy-1.3.1 && echo "" > /BUILD/installed/version-info/python/scipy \
    42  && cp /Users/aperez/software/osiris/reproduce/software/bibtex/scipy.tex /BUILD/installed/version-info/cite/ \
    43  && echo "Scipy 1.3.1 \citep{scipy2007,scipy2011}" > /BUILD/installed/version-info/python/scipy

The current 'maneage' branch of maneage has sci-py 1.5.2:

$ grep -n scipy reproduce/software/config/versions.conf
241:scipy-version = 1.5.2

So this seems to be an older version of maneage. As Mohammad said, we need to know exactly which version of maneage is being tested.

The output of the command given by Mohammad will help. The output of

git describe --always --long --dirty

would also help.

Boud Roukema <boud>
Project Member
Thu 12 Nov 2020 04:49:15 PM UTC, comment #4: 

This looks like a scipy error, not openmpi, to me:

The first compile error seems to occur here:

  9035  scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/cnaup2.f:322:5:
  9036
  9037    322 |    10 continue
  9038        |     1
  9039  Warning: Label 10 at (1) defined but not used [-Wunused-label]
  9040  scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/cnaup2.f:503:35:
  9041
  9042    392 |             call ivout (logfil, 1, iter, ndigit,
  9043        |                                   2
  9044  ......
  9045    503 |             call ivout (logfil, 3, kp, ndigit,
  9046        |                                   1
  9047  Error: Rank mismatch between actual argument at (1) and actual argument at (2) (scalar and rank-1)
  9048  scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/cnaup2.f:666:38:
  9049
  9050    392 |             call ivout (logfil, 1, iter, ndigit,
  9051        |                                   2
  9052  ......
  9053    666 |                call ivout (logfil, 2, kp, ndigit,
  9054        |                                      1
  9055  Error: Rank mismatch between actual argument at (1) and actual argument at (2) (scalar and rank-1)

and

  9098  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/dseigt.f

Maybe a macOS/Darwin fortran compiler error?

Boud Roukema <boud>
Project Member
Thu 12 Nov 2020 11:09:13 AM UTC, comment #3: 

Thanks! The uploaded file has the error messages, and we'll look into it.

But in the meantime, can you tell us what commit of Maneage you are using? You can get it with this command:

git describe --always maneage

I also corrected the title to be more clear on the nature of the problem.

Mohammad Akhlaghi <makhlaghi>
Project Administrator
Thu 12 Nov 2020 10:08:09 AM UTC, comment #2: 

Thanks for generating and sending the file. After looking at it, I noticed that it doesn't have any errors and found out that the problem was in my requested command: in the command, I had forgot to also redirect the "standard error" into the file. So the errors were actually printed on your command-line, not written into that file. In short, I should have written '&>' instead of '>'!

Sorry for my typo!

Can you please run these commands and upload the compressed file:

./project configure -e &> out.txt
gzip out.txt

Mohammad Akhlaghi <makhlaghi>
Project Administrator
Wed 11 Nov 2020 02:19:54 PM UTC, comment #1: 

Thank you for sending this bug report.

The problem is in building OpenMPI, but we need a larger portion of the output to clearly see the actual error. Can you please run this command and send us the final output ('out.txt.gz').

./project configure -e > out.txt
gzip out.txt

Mohammad Akhlaghi <makhlaghi>
Project Administrator
Wed 11 Nov 2020 10:43:28 AM UTC, original submission:  

Error in installation:
make[1]: *** [Makefile:1893: all-recursive] Error 1
make[1]: Target 'all' not remade because of errors.
make[1]: Leaving directory '/Users/aperez/software/OUTPUT/software/build-tmp/openmpi-4.0.1'
make: *** [reproduce/software/make/high-level.mk:715: /Users/aperez/software/OUTPUT/software/installed/version-info/proglib/openmpi] Error 2
make: Target 'all' not remade because of errors.

Anonymous

 

(Note: upload size limit is set to 16384 kB, after insertion of the required escape characters.)

Attach Files:
   
   
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Attached Files
file #50256:  out.txt.gz added by anampgajate (295KiB - application/x-gzip)
file #50245:  project added by None (16KiB - application/octet-stream)

 

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  • -email is unavailable- added by anampgajate (Updated the item)
  • -email is unavailable- added by makhlaghi (Posted a comment)
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    Follow 5 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2020-11-12 makhlaghi Carbon-Copy- => Added -email is unavailable-
    2020-11-12 makhlaghi SummaryProblem with ./project configure => OpenMPI fails on macOS
    2020-11-12 anampgajate Attached File- => Added out.txt.gz, #50256
    2020-11-12 makhlaghi PrivacyPrivate => Public
    2020-11-11 None Attached File- => Added project, #50245

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