Opened 10 months ago

Last modified 4 months ago

#69118 assigned defect

hdf5 @1.14.3_2+cxx+fortran+gfortran+hl+openmpi: duplicate LC_RPATH '/opt/local/lib/libgcc'

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), nsmirian (Najmeh Mirian)
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) 10 months ago.
main.log​ (75.4 KB) - added by chaochinyang (Chao-Chin Yang) 10 months ago.

Download all attachments as: .zip

Change History (8)

Changed 10 months ago by chaochinyang (Chao-Chin Yang)

Attachment: config.log​ added

Changed 10 months ago by chaochinyang (Chao-Chin Yang)

Attachment: main.log​ added

comment:1 Changed 10 months ago by jmroot (Joshua Root)

Owner: set to eborisch
Status: new → assigned
Summary: hdf5 + openmpi: config errors → hdf5 @1.14.3_2+cxx+fortran+gfortran+hl+openmpi: config errors

comment:2 Changed 10 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 9 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 #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.

For now, the only success I got is deactivating the fortran interface (e.g. the default behavior before ticket #67273), e.g. port install hdf5 +openmpi -fortran.

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

Last edited 5 months ago by ryandesign (Ryan Carsten Schmidt) (previous) (diff)

comment:4 Changed 7 months ago by Dave-Allured (Dave Allured)

Cc: Dave-Allured added

comment:5 Changed 5 months ago by matsbn (Mats Bentsen)

Cc: matsbn added

comment:6 Changed 4 months ago by ryandesign (Ryan Carsten Schmidt)

Cc: nsmirian added
Summary: hdf5 @1.14.3_2+cxx+fortran+gfortran+hl+openmpi: config errors → hdf5 @1.14.3_2+cxx+fortran+gfortran+hl+openmpi: duplicate LC_RPATH '/opt/local/lib/libgcc'

Has duplicate #70361.

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