Opened 18 months ago

Closed 17 months ago

Last modified 17 months ago

#59082 closed defect (fixed)

openmpi-gcc8 - Port is still broken after rebuilding on Max 10.14 Mojave + Xcode 11

Reported by: jmbeuken (Jean-Michel Beuken) Owned by:
Priority: Normal Milestone:
Component: ports Version: 2.6.0
Keywords: mojave Cc: majoc-at-astro (majoc-at-astro), rieder (Steven Rieder), jbgoette (Jörg Götte), jkozdon (Jeremy Kozdon), ogourgue (Olivier Gourgue), MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)
Port: openmpi-gcc8

Description (last modified by mf2k (Frank Schima))

First of all, fresh install on MacOS X 10.14 and some ports installed with success...
But :

sudo port diagnose

Error: currently installed version of Xcode, 11.0, is not supported by MacPorts.  For your currently installed system, only the following versions of Xcode are supported:  10.3 10.2.1 10.2 10.1 10.0

Warning: found dylibs in your /usr/local/lib directory. These are known to cause problems. We'd recommend  you remove them.

can this be a problem?


sudo port install openmpi-gcc8 +fortran

<snip> 2 first attemps  </snip>

--->  Cleaning openmpi-gcc8
--->  Updating database of binaries
--->  Scanning binaries for linking errors
--->  No broken files found.
--->  Found 1 broken port, determining rebuild order
--->  Rebuilding in order
     openmpi-gcc8 @4.0.1 +fortran
--->  Computing dependencies for openmpi-gcc8
--->  Fetching distfiles for openmpi-gcc8
--->  Verifying checksums for openmpi-gcc8
--->  Extracting openmpi-gcc8
--->  Applying patches to openmpi-gcc8
--->  Configuring openmpi-gcc8
--->  Building openmpi-gcc8
--->  Staging openmpi-gcc8 into destroot
--->  Deactivating openmpi-gcc8 @4.0.1_0+fortran
--->  Cleaning openmpi-gcc8
--->  Uninstalling openmpi-gcc8 @4.0.1_0+fortran
--->  Cleaning openmpi-gcc8
--->  Computing dependencies for openmpi-gcc8
--->  Installing openmpi-gcc8 @4.0.1_0+fortran
--->  Activating openmpi-gcc8 @4.0.1_0+fortran
--->  Cleaning openmpi-gcc8
--->  Updating database of binaries
--->  Scanning binaries for linking errors
--->  No broken files found.
Error: Port openmpi-gcc8 is still broken after rebuilding it more than 3 times.
Error: Please run port -d -y rev-upgrade and use the output to report a bug.
Error: rev-upgrade failed: Port openmpi-gcc8 still broken after rebuilding 3 times
Error: Follow https://guide.macports.org/#project.tickets to report a bug.
--->  Some of the ports you installed have notes:
  openmpi-gcc8 has the following notes:
    The mpicc wrapper (and friends) are installed as:
    
      /opt/local/bin/mpicc-openmpi-gcc8 (likewise mpicxx, ...)
    
    To make openmpi-gcc8's wrappers the default (what you get when
    you execute 'mpicc' etc.) please run:
    
      sudo port select --set mpi openmpi-gcc8-fortran

Here is a part of output ( full output in attachment ) after running "sudo port -d -y rev-upgrade" as suggested.

...
--->  No broken files found.
openmpi-gcc8 is using libstdc++ (this installation is configured to use libc++)
--->  Found 1 broken port, determining rebuild order
...

cfr ticket:56811

Attachments (4)

port_openmpi_gcc8.txt (54.7 KB) - added by jmbeuken (Jean-Michel Beuken) 18 months ago.
output
openmpi-gcc9.mptest14.out.gz (508.8 KB) - added by majoc-at-astro (majoc-at-astro) 17 months ago.
config.log (63.6 KB) - added by ohenrich (Oliver Henrich) 17 months ago.
configuration log
main.log (73.3 KB) - added by ohenrich (Oliver Henrich) 17 months ago.
main logfile

Download all attachments as: .zip

Change History (33)

Changed 18 months ago by jmbeuken (Jean-Michel Beuken)

Attachment: port_openmpi_gcc8.txt added

output

comment:1 Changed 18 months ago by majoc-at-astro (majoc-at-astro)

Cc: majoc-at-astro added

comment:2 Changed 18 months ago by mf2k (Frank Schima)

Description: modified (diff)

comment:3 in reply to:  description ; Changed 18 months ago by majoc-at-astro (majoc-at-astro)

Replying to jmbeuken:

--->  No broken files found.
--->  Found 1 broken port, determining rebuild order
--->  Rebuilding in order
[snip]
--->  No broken files found.
Error: Port openmpi-gcc8 is still broken after rebuilding it more than 3 times.
[snip]

We get the same round-in-circles problem with building openmpi-gcc9 with default variants, on both 10.13 and 10.14, with a freshly downloaded and updated MacPorts 2.6.0 which is otherwise empty. More details to follow (I'm offsite), but I'll try port diagnose on an empty build as soon as I'm in contact with our build servers again.

Please feel free to request other specific tests. Thanks in advance.

comment:4 in reply to:  3 Changed 17 months ago by majoc-at-astro (majoc-at-astro)

Replying to majoc-at-astro:

More details to follow (I'm offsite), but I'll try port diagnose on an empty build as soon as I'm in contact with our build servers again.

Once I remembered to add /opt/local/sbin to $PATH, port diagnose comes up empty on both test servers.

--- Ah: now I think I see at least part of the problem (please see massive attached logfile):

openmpi-gcc9 is using libstdc++ (this installation is configured to use libc++)

Curious, as this is on systems with fresh and otherwise-empty MacPorts builds. Guidance, please, folks; and apologies for repeating the original submission.

Last edited 17 months ago by majoc-at-astro (majoc-at-astro) (previous) (diff)

Changed 17 months ago by majoc-at-astro (majoc-at-astro)

comment:5 Changed 17 months ago by jmbeuken (Jean-Michel Beuken)

$echo $PATH
/opt/local/libexec/gnubin:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/buildbot/bin
$ port diagnose
Error: currently installed version of Xcode, 11.0, is not supported by MacPorts.  For your currently installed system, only the following versions of Xcode are supported:  10.3 10.2.1 10.2 10.1 10.0
Warning: found dylibs in your /usr/local/lib directory. These are known to cause problems. We'd recommend  you remove them.
Last edited 17 months ago by ryandesign (Ryan Schmidt) (previous) (diff)

comment:6 Changed 17 months ago by ryandesign (Ryan Schmidt)

We should add Xcode 11 to the list of supported versions.

You should remove what you have installed in /usr/local.

comment:7 in reply to:  6 Changed 17 months ago by jmroot (Joshua Root)

Replying to ryandesign:

We should add Xcode 11 to the list of supported versions.

Should we, with all the problems it's causing currently?

Changed 17 months ago by ohenrich (Oliver Henrich)

Attachment: config.log added

configuration log

Changed 17 months ago by ohenrich (Oliver Henrich)

Attachment: main.log added

main logfile

comment:8 Changed 17 months ago by ohenrich (Oliver Henrich)

Sorry to jump on this conversation. I see very similar problems (repeated build of a broken port -- to no avail) with older versions of Xcode (10.3 and 10.2.1). I removed the stuff in /usr/local and my port diagnose is clean.

I attached the configuration and main log of the build and would be very interested in a solution as my students and I are stuck without openmpi.

comment:9 Changed 17 months ago by ohenrich (Oliver Henrich)

PS: The issue seems to be that the C compiler can't create exectables. But when I invoke the compiler using the full path /opt/local/bin/gcc-mp-9 it works fine.

comment:10 in reply to:  6 ; Changed 17 months ago by jmbeuken (Jean-Michel Beuken)

Replying to ryandesign:

We should add Xcode 11 to the list of supported versions.

You should remove what you have installed in /usr/local.

removed..

ok for "port diagnose" :

port diagnose

Error: currently installed version of Xcode, 11.0, is not supported by MacPorts.  For your currently installed system, only the following versions of Xcode are supported:  10.3 10.2.1 10.2 10.1 10.0

but, for the build of openmpi_gcc8, not better :-(

comment:11 in reply to:  10 Changed 17 months ago by ohenrich (Oliver Henrich)

Replying to jmbeuken:

Replying to ryandesign:

We should add Xcode 11 to the list of supported versions.

You should remove what you have installed in /usr/local.

removed..

ok for "port diagnose" :

but, for the build of openmpi_gcc8, not better :-(

Have you tried an older version of Xcode? You can download them from the Apple developer portal. I tried Xcode 10.3 and 10.2.1 to no avail. Both also don't work in my case and the problem persists.

Last edited 17 months ago by ohenrich (Oliver Henrich) (previous) (diff)

comment:12 Changed 17 months ago by jbgoette (Jörg Götte)

I am sorry to chime in, but because this issue appeared first for me after installing Xcode 11, I did a fresh installation of MacOS 10.14.6 and Xcode 10.3 on a new computer I am setting up, but I still get the repeated build of a broken port openmpi-gcc9.

comment:13 Changed 17 months ago by gguillamet (Gerard Guillamet)

Hello,

Same to me. I also did a fresh installation of Xcode 10.3, but I still get the repeated build broken port for open-mpi-gcc8.

comment:14 Changed 17 months ago by rieder (Steven Rieder)

Cc: rieder added

comment:15 Changed 17 months ago by jbgoette (Jörg Götte)

Cc: jbgoette added

comment:16 Changed 17 months ago by rieder (Steven Rieder)

Same problem for me. After removing Xcode 11 and reinstalling Xcode 10.3, the problem persists...

comment:17 Changed 17 months ago by lazersos (Samuel Lazerson)

I think this may partially be a MacPorts bug. I did as others and removed XCode 11 and installed Xcode 10.3. I then attempted to download MacPorts 2.5.4. The installer text says it 2.5.4 but when it run the 'port' command it reports the code as version v2.6 not 2.5.4 and I can't seem to build openmpi-gccX (tried gcc8 and gcc9) or OpenBLAS.

comment:18 Changed 17 months ago by rieder (Steven Rieder)

I find that I can build openmpi-gcc8, and while macports insists it needs rebuilding, it seems to work fine if I just ignore that. I have the same problem with hdf5.

comment:19 Changed 17 months ago by jkozdon (Jeremy Kozdon)

Cc: jkozdon added

comment:20 Changed 17 months ago by ogourgue (Olivier Gourgue)

Cc: ogourgue added

comment:21 Changed 17 months ago by rhaas80 (Roland Haas)

Cc: rhaas80 added

comment:22 in reply to:  17 ; Changed 17 months ago by ohenrich (Oliver Henrich)

Replying to lazersos:

I think this may partially be a MacPorts bug. I did as others and removed XCode 11 and installed Xcode 10.3. I then attempted to download MacPorts 2.5.4. The installer text says it 2.5.4 but when it run the 'port' command it reports the code as version v2.6 not 2.5.4 and I can't seem to build openmpi-gccX (tried gcc8 and gcc9) or OpenBLAS.

The problem seems to be entirely down to the openmpi port. I switched to mpich-devel-gcc9 and have no issues at all.

comment:23 in reply to:  22 Changed 17 months ago by jbgoette (Jörg Götte)

Replying to ohenrich:

Replying to lazersos:

I think this may partially be a MacPorts bug. I did as others and removed XCode 11 and installed Xcode 10.3. I then attempted to download MacPorts 2.5.4. The installer text says it 2.5.4 but when it run the 'port' command it reports the code as version v2.6 not 2.5.4 and I can't seem to build openmpi-gccX (tried gcc8 and gcc9) or OpenBLAS.

The problem seems to be entirely down to the openmpi port. I switched to mpich-devel-gcc9 and have no issues at all.

That is interesting, I just tried to build mpich-devel-gcc9 from sources and ran again into the broken port issue, but if I install the binary archive it works without a problem.

Last edited 17 months ago by jbgoette (Jörg Götte) (previous) (diff)

comment:24 Changed 17 months ago by MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)

Cc: MarcusCalhoun-Lopez added

comment:25 Changed 17 months ago by MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)

By any chance, did the recent change fix this problem?
If so, another rebuild is still necessary.

comment:26 in reply to:  25 ; Changed 17 months ago by majoc-at-astro (majoc-at-astro)

Replying to MarcusCalhoun-Lopez:

By any chance, did the recent change fix this problem?
If so, another rebuild is still necessary.

It does for me in a quick test build. (I would have seen it earlier if I hadn't tripped over an interesting dependency anomaly which need not detain us here.) More thorough testing to follow.

comment:27 in reply to:  26 Changed 17 months ago by rhaas80 (Roland Haas)

Replying to majoc-at-astro:

Replying to MarcusCalhoun-Lopez:

By any chance, did the recent change fix this problem?
If so, another rebuild is still necessary.

It does for me in a quick test build. (I would have seen it earlier if I hadn't tripped over an interesting dependency anomaly which need not detain us here.) More thorough testing to follow.

Yes, [ttps://github.com/macports/macports-ports/commit/31b04db7a19d7d0b5b9952943094cbca2620723e this] seems to have fixed it for me as well.

comment:28 Changed 17 months ago by MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)

Resolution: fixed
Status: newclosed

I am glad things seem to be working.
I will close this ticket as fixes.

comment:29 Changed 17 months ago by rhaas80 (Roland Haas)

Cc: rhaas80 removed
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