openmpi-default @4.1.4: error: Could not determine global symbol label prefix

[chaochinyang (Chao-Chin Yang)]

Failed to configure openmpi-default after recent update of Xcode to 15.0:

configure:7146: /usr/bin/clang -E -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk conftest.c
conftest.c:10:10: fatal error: 'ac_nonexistent.h' file not found
#include <ac_nonexistent.h>
         ^~~~~~~~~~~~~~~~~~
1 error generated.

[chaochinyang (Chao-Chin Yang)]

config log

[chaochinyang (Chao-Chin Yang)]

main log

[ryandesign (Ryan Carsten Schmidt)]

The real error message in the main.log was:

:info:configure configure: error: Could not determine global symbol label prefix

However I don't see an obvious reason for that in the config.log. Maybe an earlier error caused it.

[mmphys]

I have the same failure (on arm64 fwiw).

:info:configure configure: error: Could not determine global symbol label prefix

Seemingly because of an objdump failure 4 lines earlier in the log

:info:configure checking if .note.GNU-stack is needed... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/objdump: error: 'conftest.o': Invalid/Unsupported object file format

I gather MacPorts is executing objdump -x file. I tried objdump -x and --file-headers, but this fails on any object file, even an empty command line tool project, e.g.:

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/objdump --file-headers main.o

main.o:	file format mach-o arm64
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/objdump: error: 'main.o': Invalid/Unsupported object file format

Assuming the image being checked was built by Xcode clang and is a mach-o (which is true in my case) presumably this openmpi-default configure test should use otool instead of objdump?

There's obviously a lot of history about objdump vs otool I'm not up to speed on ...

[gfiumara (Greg Fiumara)]

A ​patch landed upstream in 4.1.6, which resolves this issue for me under macOS 14.0 Sonoma with Xcode 15 on Apple M1. I submitted a ​pull request for this.

[ryandesign (Ryan Carsten Schmidt)]

Has duplicate #68552.

[ryandesign (Ryan Carsten Schmidt)]

Has duplicate #68641.

[isolated-matrix]

Apologies if this is a stupid question (I can work my way around the command line/terminal, but I have very little experience in programming and coding, so I want to make sure I'm understanding this correctly), but does this mean there is no fix for installing openMPI through MacPorts yet?

In #68552, it is suggested that there is a fix, but I don't see any workarounds here. Is the fix just to compile openMPI manually using the patched code linked above? Because it doesn't look like that's been approved yet.

[namus (Suman Chakrabarty)]

Same problem

[isolated-matrix]

Is the 4.1.6 update going to make it to MacPorts?

[mascguy (Christopher Nielsen)]

Replying to isolated-matrix:

Is the 4.1.6 update going to make it to MacPorts?

Definitely, I've simply been buried with work for my day job. But will try to make time over the next few weeks.

I'm so sorry for the delay on this folks!

[carlodefalco]

portfile for openmpi 4.1.6

[carlodefalco]

I tried to just bump the version to 4.1.6 in the portfile and it installed fine for me in sonoma/M2 the updated portfile is attached attachment:Portfile​

[willic3 (Charles Williams)]

Replying to carlodefalco:

I tried to just bump the version to 4.1.6 in the portfile and it installed fine for me in sonoma/M2 the updated portfile is attached ​https://trac.macports.org/attachment/ticket/68226/Portfile

I can confirm that this portfile works for me on a mid-2018 Intel Macbook Pro running Sonoma 14.1.

[isolated-matrix]

Replying to carlodefalco:

I tried to just bump the version to 4.1.6 in the portfile and it installed fine for me in sonoma/M2 the updated portfile is attached attachment:Portfile​

I'm sorry, but I don't know how to install it from that file. Is it going to be uploaded to the MacPorts 'tree' (if that's the correct word), or are there further approval processes to go through?

[ryandesign (Ryan Carsten Schmidt)]

Has duplicate #68967.

[Michael-P-Allen (Mike Allen)]

The Portfile uploaded by @carlodefalco worked on my 2018 Intel Mac Mini running Ventura 13.6.3 with XCode 15.1. @isolated-matrix I followed the instructions at ​https://trac.macports.org/wiki/howto/Upgrade except that there is no need to edit the original Portfile, simply replace it (after making a backup copy) with the new one. I'm regarding this as a temporary workaround until a newer version finds its way into the Macports system.

[isolated-matrix]

Replying to Michael-P-Allen:

The Portfile uploaded by @carlodefalco worked on my 2018 Intel Mac Mini running Ventura 13.6.3 with XCode 15.1. @isolated-matrix I followed the instructions at ​https://trac.macports.org/wiki/howto/Upgrade except that there is no need to edit the original Portfile, simply replace it (after making a backup copy) with the new one. I'm regarding this as a temporary workaround until a newer version finds its way into the Macports system.

Ah, thank you, that worked! One thing, though... the installation didn't actually create an mpirun binary; instead, I have a series of *-openmpi-mp files in my /opt/local/bin directory. Is that what was supposed to happen, or did I do something incorrectly in my installation? I'm not sure that the programs which need OpenMPI are going to recognise those binaries...

[Michael-P-Allen (Mike Allen)]

Replying to isolated-matrix:

Replying to Michael-P-Allen:

The Portfile uploaded by @carlodefalco worked on my 2018 Intel Mac Mini running Ventura 13.6.3 with XCode 15.1. @isolated-matrix I followed the instructions at ​https://trac.macports.org/wiki/howto/Upgrade except that there is no need to edit the original Portfile, simply replace it (after making a backup copy) with the new one. I'm regarding this as a temporary workaround until a newer version finds its way into the Macports system.

Ah, thank you, that worked! One thing, though... the installation didn't actually create an mpirun binary; instead, I have a series of *-openmpi-mp files in my /opt/local/bin directory. Is that what was supposed to happen, or did I do something incorrectly in my installation? I'm not sure that the programs which need OpenMPI are going to recognise those binaries...

We should avoid cluttering this trac report, and people’s emails, with general installation issues. Nonetheless (apologies all) I believe that this is expected behaviour. At the end of the installation, a usage note will have appeared, saying that you should do something like sudo port select --set mpi openmpi-mp-fortran to make the Macports binaries the default ones. But please check this yourself to be sure.

[Christopher Nielsen <mascguy@…>]

In 74d90db04674fb5750552aa68598e9bb6612da36/macports-ports (master):

openmpi: update to 4.1.6

Fixes: #68226