[MacPorts] #48825: dolfin @1.6.0_0 +openmpi +suitesparse fails to build
#48825: dolfin @1.6.0_0 +openmpi +suitesparse fails to build ----------------------------+-------------------------------- Reporter: mschamschula@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: | Port: dolfin ----------------------------+-------------------------------- The update to dolfin 1.6.0 (+openmpi +suitesparse variant) fails to build while compiling modulePYTHON_wrap.cxx. main.log attached. I have had two Yosemite machines fail the same way. -- Ticket URL: <https://trac.macports.org/ticket/48825> MacPorts <https://www.macports.org/> Ports system for OS X
#48825: dolfin @1.6.0_0 +openmpi +suitesparse fails to build -----------------------------+-------------------- Reporter: mschamschula@… | Owner: sean@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: dolfin | -----------------------------+-------------------- Changes (by petr@…): * owner: macports-tickets@… => sean@… * cc: sean@… (removed) -- Ticket URL: <https://trac.macports.org/ticket/48825#comment:1> MacPorts <https://www.macports.org/> Ports system for OS X
#48825: dolfin @1.6.0_0 +openmpi +suitesparse fails to build -----------------------------+-------------------- Reporter: mschamschula@… | Owner: sean@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: dolfin | -----------------------------+-------------------- Comment (by sean@…): I just installed this and had no problems. Do you have anything installed in `/usr/local`? The log file suggests some weird things going on with c++ (perhaps stdc++ issues?). I dunno. Maybe boost is throwing in the wrong libs? -- Ticket URL: <https://trac.macports.org/ticket/48825#comment:2> MacPorts <https://www.macports.org/> Ports system for OS X
#48825: dolfin @1.6.0_0 +openmpi +suitesparse fails to build -----------------------------+-------------------- Reporter: mschamschula@… | Owner: sean@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: dolfin | -----------------------------+-------------------- Comment (by mschamschula@…): Replying to [comment:2 sean@…]:
I just installed this and had no problems. Do you have anything installed in `/usr/local`? The log file suggests some weird things going on with c++ (perhaps stdc++ issues?). I dunno. Maybe boost is throwing in the wrong libs?
Nope. Nothing in /usr/local. {{{port installed boost}}} gives me {{{boost @1.59.0_1+mpich+no_single+no_static+python27}}} -- Ticket URL: <https://trac.macports.org/ticket/48825#comment:3> MacPorts <https://www.macports.org/> Ports system for OS X
#48825: dolfin @1.6.0_0 +openmpi +suitesparse fails to build -----------------------------+-------------------- Reporter: mschamschula@… | Owner: sean@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: fixed | Keywords: Port: dolfin | -----------------------------+-------------------- Changes (by sean@…): * status: new => closed * resolution: => fixed Comment: Replying to [comment:3 mschamschula@…]:
Replying to [comment:2 sean@…]:
I just installed this and had no problems. Do you have anything installed in `/usr/local`? The log file suggests some weird things going on with c++ (perhaps stdc++ issues?). I dunno. Maybe boost is throwing in the wrong libs?
Nope. Nothing in /usr/local.
{{{port installed boost}}} gives me {{{boost @1.59.0_1+mpich+no_single+no_static+python27}}}
This should have been caught by `mpi` portgroup. You need to match the same `mpi` variants with `boost` and its descendants due to the fact that mpi is a compiler wrapper. I'm going to mark this as invalid but if my advice of installing `dolfin +mpich` doesn't work, feel free to reopen. -- Ticket URL: <https://trac.macports.org/ticket/48825#comment:4> MacPorts <https://www.macports.org/> Ports system for OS X
#48825: dolfin @1.6.0_0 +openmpi +suitesparse fails to build -----------------------------+-------------------- Reporter: mschamschula@… | Owner: sean@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: fixed | Keywords: Port: dolfin | -----------------------------+-------------------- Comment (by mschamschula@…): Hmm. When I initially installed dolfin it also installed mpich, as that is the dolfin default variant (+mpich +suitesparse). So when I attempted to upgrade dolfin to 1.6.0 I ran into this issue. After cleaning out dolfin (and its particular dependencies) I just attempted to install dolfin. This time I manually set +mpich (redundant, but just make sure). The results (errors) are the same, even though the parallel build job got terminated in a different order. -- Ticket URL: <https://trac.macports.org/ticket/48825#comment:5> MacPorts <https://www.macports.org/> Ports system for OS X
#48825: dolfin @1.6.0_0 +openmpi +suitesparse fails to build -----------------------------+---------------------- Reporter: mschamschula@… | Owner: sean@… Type: defect | Status: reopened Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: | Keywords: Port: dolfin | -----------------------------+---------------------- Changes (by sean@…): * status: closed => reopened * resolution: fixed => Comment: Well, damn. There seems to be weird things with `libc++` and `julia`. -- Ticket URL: <https://trac.macports.org/ticket/48825#comment:6> MacPorts <https://www.macports.org/> Ports system for OS X
#48825: dolfin @1.6.0_0 +openmpi +suitesparse fails to build -----------------------------+-------------------- Reporter: mschamschula@… | Owner: sean@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: fixed | Keywords: Port: dolfin | -----------------------------+-------------------- Changes (by sean@…): * status: reopened => closed * resolution: => fixed Comment: I just dug this up again. I think it's happening because one of your dependency ports was built with gcc. If you can ensure they are all built with clang, then I think that was fix it. -- Ticket URL: <https://trac.macports.org/ticket/48825#comment:7> MacPorts <https://www.macports.org/> Ports system for OS X
#48825: dolfin @1.6.0_0 +openmpi +suitesparse fails to build -----------------------------+-------------------- Reporter: mschamschula@… | Owner: sean@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: fixed | Keywords: Port: dolfin | -----------------------------+-------------------- Comment (by mschamschula@…): Replying to [comment:7 sean@…]:
I just dug this up again. I think it's happening because one of your dependency ports was built with gcc. If you can ensure they are all built with clang, then I think that was fix it.
In other words, use +accelerate, rather than +atlas to build SuiteSparse? atlas is built using gcc by default. After all, my only reason to build dolfin was as a prerequisite for octave-fem-fenics. -- Ticket URL: <https://trac.macports.org/ticket/48825#comment:8> MacPorts <https://www.macports.org/> Ports system for OS X
#48825: dolfin @1.6.0_0 +openmpi +suitesparse fails to build -----------------------------+-------------------- Reporter: mschamschula@… | Owner: sean@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: fixed | Keywords: Port: dolfin | -----------------------------+-------------------- Comment (by sean@…): Replying to [comment:8 mschamschula@…]:
Replying to [comment:7 sean@…]:
I just dug this up again. I think it's happening because one of your dependency ports was built with gcc. If you can ensure they are all built with clang, then I think that was fix it.
In other words, use +accelerate, rather than +atlas to build SuiteSparse?
atlas is built using gcc by default.
After all, my only reason to build dolfin was as a prerequisite for octave-fem-fenics.
That *should* be alright but you can try to use clang to build atlas. I was more worried about something using gcc's c++ library as opposed to clang (since they are incompatible). `boost` smells suspicious but I can't really tell for sure. -- Ticket URL: <https://trac.macports.org/ticket/48825#comment:9> MacPorts <https://www.macports.org/> Ports system for OS X
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