#42244: openmpi-default not compiling using clang on Mac OSX 10.6.8 -------------------------+---------------------- Reporter: andrewhw@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: | -------------------------+---------------------- Comment (by sean@…): I don't know if the description has a typo but this error is for openmpi- default (which makes sense because before my update of macports there was no openmpi-devel port). Could you attach config.log from `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_openmpi /openmpi-default/work/build/opal/mca/event/libevent2021/libevent`? It might be in a directory above that. Also, the buildbot should have this port for binary download now, so maybe you could use that? (just rerun the upgrade command) -- Ticket URL: <https://trac.macports.org/ticket/42244#comment:2> MacPorts <http://www.macports.org/> Ports system for OS X

#42244: openmpi-default not compiling using clang on Mac OSX 10.6.8 -------------------------+---------------------- Reporter: andrewhw@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: | -------------------------+---------------------- Comment (by sean@…): Something is very wrong here. For one, the work directory is 'openmpi- default' which should be 'openmpi-devel-default'. Second, it's missing the hwloc dependency which should be installed automatically. Third, you said this comes from 'port upgrade outdated' which isn't possible since I added that in r116342. Are you using a local source which provides openmpi- devel? -- Ticket URL: <https://trac.macports.org/ticket/42244#comment:4> MacPorts <http://www.macports.org/> Ports system for OS X

#42244: openmpi-default not compiling using clang on Mac OSX 10.6.8 -------------------------+---------------------- Reporter: andrewhw@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: | -------------------------+---------------------- Comment (by sean@…): Right, so as I thought you only have openmpi installed, not openmpi-devel. Where is openmpi-devel coming from? Either way, it should be configuring so maybe the old openmpi is conflicting with it? Could you try deactivating it first and see if configure goes through after that? -- Ticket URL: <https://trac.macports.org/ticket/42244#comment:6> MacPorts <http://www.macports.org/> Ports system for OS X

#42244: openmpi-default not compiling using clang on Mac OSX 10.6.8 ------------------------------+---------------------- Reporter: andrewhw@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: openmpi-default | ------------------------------+---------------------- Changes (by macsforever2000@…): * port: => openmpi-default -- Ticket URL: <https://trac.macports.org/ticket/42244#comment:8> MacPorts <http://www.macports.org/> Ports system for OS X

#42244: openmpi-default not compiling using clang on Mac OSX 10.6.8 ------------------------------+---------------------- Reporter: andrewhw@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: openmpi-default | ------------------------------+---------------------- Comment (by andrewhw@…): ... and looking above, my correction from "openmpi-devel -> openmpi- default" was itself a miscorrection. While I am sure I have seen the string "openmpi-devel" somewhere in poking through the logs, you are quite right in stating that we are only looking at "openmpi-default", and my earlier attempt at clarification simply re-affirmed the error through bad typing/proofreading. -- Ticket URL: <https://trac.macports.org/ticket/42244#comment:10> MacPorts <http://www.macports.org/> Ports system for OS X

#42244: openmpi-default not compiling using clang on Mac OSX 10.6.8 ------------------------------+---------------------- Reporter: andrewhw@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: openmpi-default | ------------------------------+---------------------- Comment (by andrewhw@…): Still no success. Clean is good: {{{ % sudo port clean openmpi-default ---> Cleaning openmpi-default % }}} but configure doesn't succeed {{{ % sudo port configure openmpi-default ---> Computing dependencies for openmpi-default ---> Fetching distfiles for openmpi-default ---> Verifying checksums for openmpi-default ---> Extracting openmpi-default ---> Configuring openmpi-default Error: Failed to configure openmpi-default, consult /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_openmpi /openmpi-default/work/build/config.log Error: org.macports.configure for port openmpi-default returned: configure failure: command execution failed Please see the log file for port openmpi-default for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_openmpi /openmpi-default/main.log To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port openmpi-default failed % }}} In addition, I'm not sure which log you mean, as I don't have any log file in that directory: {{{ % ls /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_openmpi /openmpi- default/work/openmpi-1.7.3/opal/mca/event/libevent2021/libevent/*.log ls: No match. % ls /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_openmpi /openmpi- default/work/openmpi-1.7.3/opal/mca/event/libevent2021/libevent*/*.log ls: No match. % }}} Perhaps you meant the config log again? I'll upload it and tag it "v3"... -- Ticket URL: <https://trac.macports.org/ticket/42244#comment:12> MacPorts <http://www.macports.org/> Ports system for OS X

#42244: openmpi-default not compiling using clang on Mac OSX 10.6.8 ------------------------------+---------------------- Reporter: andrewhw@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: openmpi-default | ------------------------------+---------------------- Comment (by sean@…): Thanks again! The error still seems to be hwloc: {{{ ld: library not found for -lhwloc }}} What does hwloc show for its libraries? Here is what I have: {{{ $ port contents hwloc | grep /lib /opt/local/lib/libhwloc.5.dylib /opt/local/lib/libhwloc.dylib /opt/local/lib/libhwloc.la /opt/local/lib/pkgconfig/hwloc.pc }}} -- Ticket URL: <https://trac.macports.org/ticket/42244#comment:14> MacPorts <http://www.macports.org/> Ports system for OS X

#42244: openmpi-default not compiling using clang on Mac OSX 10.6.8 ------------------------------+---------------------- Reporter: andrewhw@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: openmpi-default | ------------------------------+---------------------- Comment (by andrewhw@…): Strangely, this is the same: {{{ % port contents hwloc | grep /lib /opt/local/lib/libhwloc.5.dylib /opt/local/lib/libhwloc.dylib /opt/local/lib/libhwloc.la /opt/local/lib/pkgconfig/hwloc.pc % }}} For filetimes I have this: {{{ % ls -l `!!` ls -l `port contents hwloc | grep /lib` -rwxr-xr-x 1 root admin 152072 Nov 29 19:41 /opt/local/lib/libhwloc.5.dylib lrwxr-xr-x 1 root admin 16 Nov 29 19:41 /opt/local/lib/libhwloc.dylib -> libhwloc.5.dylib -rwxr-xr-x 1 root admin 923 Nov 29 19:41 /opt/local/lib/libhwloc.la -rw-r--r-- 1 root admin 285 Nov 29 19:41 /opt/local/lib/pkgconfig/hwloc.pc % }}} -- Ticket URL: <https://trac.macports.org/ticket/42244#comment:16> MacPorts <http://www.macports.org/> Ports system for OS X

#42244: openmpi-default not compiling using clang on Mac OSX 10.6.8 ------------------------------+---------------------- Reporter: andrewhw@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: openmpi-default | ------------------------------+---------------------- Comment (by sean@…): Ok, well, I figured out the problem: https://trac.macports.org/browser/trunk/dports/science/openmpi/Portfile?rev=... The port deletes ${prefix}/lib to prevent linking to a previous version already installed. The strange part is why my version worked … Well, anyway, I will test to make sure version >=1.7 don't link against a previously installed version of openmpi and get back to you. -- Ticket URL: <https://trac.macports.org/ticket/42244#comment:18> MacPorts <http://www.macports.org/> Ports system for OS X

#42244: openmpi-default not compiling using clang on Mac OSX 10.6.8 ------------------------------+---------------------- Reporter: andrewhw@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: openmpi-default | ------------------------------+---------------------- Comment (by andrewhw@…): Some improvement! I ran the following, and all was well: {{{ % sudo port clean openmpi-default % sudo port configure openmpi-default }}} After that I tried this: {{{ % sudo port configure openmpi-default }}} and was told that it wanted a specific version, so I tried this: {{{ % sudo port activate "octave @3.6.4_10+atlas+gcc47" ---> Activating octave @3.6.4_10+atlas+gcc47 }}} which looked good, so I continued with {{{ % sudo port activate arpack ---> Computing dependencies for arpack ---> Dependencies to be installed: openmpi ---> Fetching distfiles for openmpi ---> Verifying checksums for openmpi ---> Extracting openmpi ---> Configuring openmpi Error: openmpi has been made obsolete by the port openmpi-default. Please install openmpi-default instead. Error: org.macports.configure for port openmpi returned: obsolete port Error: Failed to install openmpi Please see the log file for port openmpi for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_openmpi/openmpi/main.log Error: The following dependencies were not installed: openmpi Warning: Failed to execute portfile from registry for arpack @3.1.3_0+accelerate+openmpi ---> Activating arpack @3.1.3_0+accelerate+openmpi % }}} at this point, it seemed sensible to install "openmpi-default", so I did that: {{{ % sudo port install "openmpi-default" ---> Computing dependencies for openmpi-default ---> Building openmpi-default ---> Staging openmpi-default into destroot ---> Installing openmpi-default @1.7.3_2+gcc48 ---> Activating openmpi-default @1.7.3_2+gcc48 +--- OpenMPI Usage note ---- | The mpi[cc|cxx|f77|f90] weappers are installed as | mpi[cc|cxx|f77|f90]-mp. To make openmpi-default the default (i.e. the | version you get when you run 'mpicc/mpicxx'), please run: | | sudo port select --set mpi openmpi-mp-fortran +------------------------- ---> Cleaning openmpi-default ---> Updating database of binaries: 100.0% ---> Scanning binaries for linking errors: 100.0% ---> Found 6 broken file(s), matching files to ports ---> Found 1 broken port(s), determining rebuild order ---> Rebuilding in order arpack @3.1.3 +accelerate+openmpi ---> Computing dependencies for arpack ---> Fetching archive for arpack ---> Attempting to fetch arpack-3.1.4_1+accelerate+gfortran+openmpi.darwin_10.x86_64.tbz2 from http://lil.fr.packages.macports.org/arpack ---> Attempting to fetch arpack-3.1.4_1+accelerate+gfortran+openmpi.darwin_10.x86_64.tbz2 from http://packages.macports.org/arpack ---> Attempting to fetch arpack-3.1.4_1+accelerate+gfortran+openmpi.darwin_10.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/arpack ---> Fetching distfiles for arpack ---> Attempting to fetch arpack-ng_3.1.4.tar.gz from http://ykf.ca.distfiles.macports.org/MacPorts/mpdistfiles/arpack ---> Verifying checksums for arpack ---> Extracting arpack ---> Applying patches to arpack ---> Configuring arpack ---> Building arpack Error: org.macports.build for port arpack returned: command execution failed Please see the log file for port arpack for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_arpack/arpack/main.log Error: Unable to upgrade port: 1 Error rebuilding arpack while executing "error "Error rebuilding $portname"" (procedure "revupgrade_scanandrebuild" line 382) invoked from within "revupgrade_scanandrebuild broken_port_counts $opts" (procedure "macports::revupgrade" line 5) invoked from within "macports::revupgrade $opts" (procedure "action_revupgrade" line 2) invoked from within "action_revupgrade $action $portlist $opts" (procedure "action_target" line 96) invoked from within "$action_proc $action $portlist [array get global_options]" (procedure "process_cmd" line 93) invoked from within "process_cmd $remaining_args" invoked from within "if { [llength $remaining_args] > 0 } { # If there are remaining arguments, process those as a command set exit_status [process_cmd $remaining..." (file "/opt/local/bin/port" line 4857) % }}} ... so have I lost the path in there? Should I be running the "port select" line? Or is openmpi now no longer the problem and I have triggered something new in arpack? I will note that I earlier received a warning about switching arpack from +accelerate to +atlas to avoid triggering a floating point bug on Apple, but have not yet done that as I feel that concurrent changes will only confuse thing further. I am attaching the arpack log file, as well as the results of "port list inactive"... -- Ticket URL: <https://trac.macports.org/ticket/42244#comment:20> MacPorts <http://www.macports.org/> Ports system for OS X

#42244: openmpi-default not compiling using clang on Mac OSX 10.6.8 ------------------------------+-------------------- Reporter: andrewhw@… | Owner: sean@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: fixed | Keywords: Port: openmpi-default | ------------------------------+-------------------- Changes (by sean@…): * status: assigned => closed * resolution: => fixed Comment: You will probably have to uninstall the dependents of openmpi since ports built against the old version won't work. {{{ $ sudo port uninstall --follow-dependents openmpi and installed $ sudo port uninstall --follow-dependents openmpi-default }}} Then reinstall openmpi-default, {{{ $ sudo port install openmpi-default }}} if that works, continue with arpack and octave. I'm going to close the ticket because I'm pretty sure that will fix this error but if something else is still wrong, definitely report back. -- Ticket URL: <https://trac.macports.org/ticket/42244#comment:22> MacPorts <http://www.macports.org/> Ports system for OS X