Opened 5 months ago

Last modified 4 days ago

#69118 assigned defect

hdf5 @1.14.3_2+cxx+fortran+gfortran+hl+openmpi: config errors

Reported by: chaochinyang (Chao-Chin Yang) Owned by: eborisch (Eric A. Borisch)
Priority: Normal Milestone:
Component: ports Version: 2.8.1
Keywords: Cc: Dave-Allured (Dave Allured), matsbn (Mats Bentsen)
Port: hdf5

Description

I am trying to build parallel HDF5 with openmpi:

sudo port install hdf5 +openmpi

but it failed at config stage. It appears to be related with the code conftest.c.

I am using macports on my 16-inch MacBook Pro with M1 Max and latest macOS 14.2.1 (23C71).

Log files will be attached.

Attachments (2)

config.log (132.5 KB) - added by chaochinyang (Chao-Chin Yang) 5 months ago.
main.log (75.4 KB) - added by chaochinyang (Chao-Chin Yang) 5 months ago.

Download all attachments as: .zip

Change History (7)

Changed 5 months ago by chaochinyang (Chao-Chin Yang)

Attachment: config.log added

Changed 5 months ago by chaochinyang (Chao-Chin Yang)

Attachment: main.log added

comment:1 Changed 5 months ago by jmroot (Joshua Root)

Owner: set to eborisch
Status: newassigned
Summary: hdf5 + openmpi: config errorshdf5 @1.14.3_2+cxx+fortran+gfortran+hl+openmpi: config errors

comment:2 Changed 5 months ago by kencu (Ken)

errors: duplicate LC_RPATH '/opt/local/lib/libgcc' in '/opt/local/lib/openmpi-mp/libmpi_usempi_ignore_tkr.40.dylib

comment:3 Changed 4 months ago by jmon12

I've had the similar issue with openmpi-default:

:info:configure configure: error: linking to Fortran libraries from C fails

I've tried the following combinations:

  • openmpi-gcc13 and hdf5 +openmpi +gcc13 --> Fail to install openmpi-gcc13, see ticket https://trac.macports.org/ticket/68837
  • openmpi-clang17 and hdf5 +openmpi +clang17 --> Fails to configure (like openmpi-default)
  • openmpi-gcc12 and hdf5 +openmpi +gcc12 --> Fails to build (the final or an intermediary linking step). I need to investigate further.

Note that in any case, I'm setting openmpi's wrapper (see port notes openmpi-<compiler>), for example for gcc12: sudo port select --set mpi openmpi-gcc12-fortran. Anyway it shouldn't play a role.

I'm using a MacBook Pro (2020) with intel CPU and MacOS 14.3.1 (23D60).

Version 0, edited 4 months ago by jmon12 (next)

comment:4 Changed 6 weeks ago by Dave-Allured (Dave Allured)

Cc: Dave-Allured added

comment:5 Changed 4 days ago by matsbn (Mats Bentsen)

Cc: matsbn added
Note: See TracTickets for help on using tickets.