py-graph-tool fails to build with clang OpenMP option (configure.args=--enable-openmp)

[essandess (Steve Smith)]

Macports clang 3.7 and 3.8 now support OpenMP, which creates the opportunity to build graph-tool on OS X with OpenMP speeds.

I expected that the option configure.args=--enable-openmp would tell the autoconf'd ./configure command to specify --enable-openmp, but it does not:

# uninstall existing graph-tool
sudo port uninstall py-graph-tool py27-graph-tool
sudo port clean --dist py-graph-tool py27-graph-tool

# build new graph-tool with OpenMP support
sudo port install clang-3.8 +openmp
sudo port -d install py-graph-tool py27-graph-tool configure.compiler=macports-clang-3.8 configure.args=--enable-openmp

…
DEBUG: Executing command line: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_python_py-graph-tool/py27-graph-tool/work/graph-tool-2.13" && ./configure --prefix=/opt/local --with-boost=/opt/local --exec-prefix=/opt/local/Library/Frameworks/Python.framework/Versions/2.7
…
checking whether to enable parallel algorithms with openmp... no

The port notes for libomp say:

Use with clang-3.[78] (when built with +openmp variant) by adding
"-fopenmp" to your compile and link lines.
(Or "-I/opt/local/include/libomp -L/opt/local/lib/libomp -fopenmp"
if clang is installed without +openmp.)

Based on the Port Phases page ​https://guide.macports.org/chunked/reference.phases.htm, I've tried a variety of options like configure.cxxflags-append=-fopenmp, all without success.

I'd also ask for consideration whether adding OpenMP support should be the default behavior for the Macports graph-tool build now that it's available.

[mamoll (Mark Moll)]

Can you change the Portfile like so:

Index: Portfile
===================================================================
--- Portfile	(revision 147061)
+++ Portfile	(working copy)
@@ -81,7 +81,7 @@
     }
     configure.cppflags-append -I${prefix}/include -I${python.include}/..
     configure.ldflags-append -L${prefix}/lib
-    configure.args-append --with-boost=${prefix} --exec-prefix=${python.prefix}
+    configure.args-append --with-boost=${prefix} --exec-prefix=${python.prefix} --enable-openmp
     # Clang uses the old libstc++ from gcc 4.2 before OS X 10.9. Boost doesn't
     # include some of the tr1 headers in libstdc++ and defines its own tr1
     # classes. This causes conflicts with sparsehash which insists on using

That seems to work for me. On my machine there is no +openmp variant for clang-3.8 (it's included by default). The clang-3.7 *does* has an +openmp variant. The version of clang that comes with the latest Xcode doesn't support openmp at all. How do I do the right thing in all cases?

[essandess (Steve Smith)]

After applying this patch, clang-3.8 fails with the error

In file included from graph_blockmodel.cc:39:
In file included from ./graph_blockmodel_overlap.hh:24:
./graph_blockmodel.hh:2708:43: warning: missing ':' after directive name modifier - ignoring [-Wignored-pragmas]
            schedule(runtime) if (parallel)
                                          ^
./graph_blockmodel.hh:2708:43: error: expected expression

I'll go try clang-3.7...

[mamoll (Mark Moll)]

If compilation fails, you might want to file a ticket upstream at ​https://git.skewed.de/count0/graph-tool/issues/.

[essandess (Steve Smith)]

On my system clang-3.7 fails with this error:

In file included from graph_betweenness.cc:20:
In file included from /opt/local/include/boost/python.hpp:41:
/opt/local/include/boost/python/make_constructor.hpp:177:32: warning: unused typedef 'assertion' [-Wunused-local-typedef]
          >::too_many_keywords assertion;
                               ^
fatal error: error in backend: Cannot select: 0x7fe332ed22a0: f80 = zero_extend 0x7fe332ed1e00 [ORD=3] [ID=4]
  0x7fe332ed1e00: i64 = FrameIndex<14> [ID=1]
In function: .omp_outlined..24
clang: error: clang frontend command failed with exit code 70 (use -v to see invocation)

The build commands are:

sudo port install clang-3.7 +openmp
sudo port -d install py-graph-tool configure.compiler=macports-clang-3.7

[count0 (Tiago de Paula Peixoto)]

Replying to s.t.smith@…:

After applying this patch, clang-3.8 fails with the error

In file included from graph_blockmodel.cc:39:
In file included from ./graph_blockmodel_overlap.hh:24:
./graph_blockmodel.hh:2708:43: warning: missing ':' after directive name modifier - ignoring [-Wignored-pragmas]
            schedule(runtime) if (parallel)
                                          ^
./graph_blockmodel.hh:2708:43: error: expected expression

This seems like a perfectly valid OpenMP annotation to me...

[essandess (Steve Smith)]

Replying to tiago@…:

This seems like a perfectly valid OpenMP annotation to me...

Sounds like the upstream ticket should go to clang. I'll post one there.

[essandess (Steve Smith)]

Replying to s.t.smith@…:

Replying to tiago@…:

This seems like a perfectly valid OpenMP annotation to me...

Sounds like the upstream ticket should go to clang. I'll post one there.

Oh wait -- there's a clang-3.9. I'll attempt compiling with the latest version.

[essandess (Steve Smith)]

Still no luck with clang-3.9. Same error as above with 3.8:

In file included from graph_blockmodel.cc:39:
In file included from ./graph_blockmodel_overlap.hh:24:
./graph_blockmodel.hh:2708:43: warning: missing ':' after directive name modifier - ignoring [-Wignored-pragmas]
            schedule(runtime) if (parallel)
                                          ^
./graph_blockmodel.hh:2708:43: error: expected expression
In file included from graph_blockmodel.cc:39:
./graph_blockmodel_overlap.hh:1337:67: warning: missing ':' after directive name modifier - ignoring [-Wignored-pragmas]
            firstprivate(m_entries) schedule(runtime) if (parallel)
                                                                  ^
./graph_blockmodel_overlap.hh:1337:67: error: expected expression
In file included from graph_blockmodel.cc:39:
In file included from ./graph_blockmodel_overlap.hh:24:
In file included from ./graph_blockmodel.hh:26:

I'll post bug report to clang.

[essandess (Steve Smith)]

Upstreamed to ticket ​https://trac.macports.org/ticket/50983

[essandess (Steve Smith)]

The feedback from the upstream ticket mentions that omp's parallel if clause has a "parallel"-named qualifier, which causes the compilation problem. ​https://trac.macports.org/ticket/50983#comment:8

I confirm that replacing the variable name "parallel" with "parallel_enabled" yields a successful compile. Patch files attached.

Replying to larryv@…:

​Clang supports directive name modifiers in OpenMP 4.5 if clauses. From §2.12 of the ​OpenMP 4.5 spec:

The syntax of the if clause is as follows:

if([directive-name-modifier :]scalar-expression)

And from §2.5:

The syntax of the parallel construct is as follows:

#pragma omp parallel [clause[[,]clause]...]new-line
structured-block

where clause is one of the following:

if([parallel :]scalar-expression)

…

This seems to make “parallel” a sort of reserved word that requires a trailing colon, so I doubt LLVM upstream would consider this a bug, although you’re free to ​submit a report. I suggest that graph-tool simply use any other variable name.

[essandess (Steve Smith)]

Patch file to replace variable name "parallel" with "parallel_enabled"

[essandess (Steve Smith)]

Patch file to replace variable name "parallel" with "parallel_enabled"

[essandess (Steve Smith)]

Once Tiago agrees, this gets us back to the original problem: adding OpenMP support to the py-graph-tool port.

Adding the "port" command line argument "configure.args=--enable-openmp" or "configure.args-append=--enable-openmp" doesn't append "--enable-openmp" to "./configure".

[mamoll (Mark Moll)]

Thanks for the patches. Something like this works for clang 3.[89]:

if {${configure.compiler} eq "macports-clang-3.8" ||
    ${configure.compiler} eq "macports-clang-3.9"} {
      configure.args-append --enable-openmp
}

but I can't distinguish between clang-3.7 and clang-3.7+openmp, so it seems safest to assume the clang-3.7 doesn't support OpenMP.

[count0 (Tiago de Paula Peixoto)]

Replying to s.t.smith@…:

I confirm that replacing the variable name "parallel" with "parallel_enabled" yields a successful compile. Patch files attached.

These patches seem fine. Please submit them as well to the upstream repository at: ​https://git.skewed.de/count0/graph-tool

[essandess (Steve Smith)]

Replying to mmoll@…:

Thanks for the patches. Something like this works for clang 3.[89]:

if {${configure.compiler} eq "macports-clang-3.8" ||
    ${configure.compiler} eq "macports-clang-3.9"} {
      configure.args-append --enable-openmp
}

but I can't distinguish between clang-3.7 and clang-3.7+openmp, so it seems safest to assume the clang-3.7 doesn't support OpenMP.

I'm testing with the latest upgrades and have run into the problem that clang_select shows "mp-clang-3.9", *not* "macports-clang-3.9":

$ sudo port select --list clang
Available versions for clang:
	mp-clang-3.9 (active)
	none
$ sudo port select --set clang macports-clang-3.9
Selecting 'macports-clang-3.9' for 'clang' failed: The specified version 'macports-clang-3.9' is not valid.
$ sudo port select --set clang mp-clang-3.9
Selecting 'mp-clang-3.9' for 'clang' succeeded. 'mp-clang-3.9' is now active.

The current port file doesn't detect that I've set clang-3.9 to be the default:

sudo port -d install py-graph-tool
...
checking whether to enable parallel algorithms with openmp... no

I've also confirmed that if I edit the port file to say the following, --enable-openmp is not passed to ./configure:

    if {${configure.compiler} eq "mp-clang-3.8" ||
        ${configure.compiler} eq "mp-clang-3.9"} {
        configure.args-append --enable-openmp
    }

Then this:

sudo port -d install py-graph-tool
...
checking whether to enable parallel algorithms with openmp... no

If I pass the command line argument configure.args-append=--enable-openmp, the argument is not passed:

sudo port -d install py-graph-tool configure.args-append=--enable-openmp
...
checking whether to enable parallel algorithms with openmp... no

If I change the port file back to its original, then the --enable-openmp argument is passed with the command. This is the only thing that's working so far:

sudo port -d install py-graph-tool configure.compiler=macports-clang-3.9
...
DEBUG: Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_python_py-graph-tool/py27-graph-tool/work/graph-tool-2.13" && ./configure --prefix=/opt/local --with-boost=/opt/local --exec-prefix=/opt/local/Library/Frameworks/Python.framework/Versions/2.7 --enable-openmp'
...
checking whether to enable parallel algorithms with openmp... yes

[essandess (Steve Smith)]

Tiago's update from this ticket ​https://git.skewed.de/count0/graph-tool/issues/289 is already reflected in the mirrors, so all that's needed now is for the portfile to pass --enable-openmp to ./configure.

[mamoll (Mark Moll)]

I don't think port select clang ... changes the default compiler that MacPorts uses. It just creates symlinks so that clang points to clang-3.9. You can change the compiler by specifying it in ${prefix}/etc/macports/macports.conf. This shouldn't be necessary:

 configure.args-append=--enable-openmp

It's already part of the Portfile.

[essandess (Steve Smith)]

Is there a setting that will allow

sudo port upgrade outdated

or

sudo port install py-graph-tool

to automatically compile graph-tool upgrades with OpenMP support, without having to pass a configure.compiler=macports-clang-3.9 by hand?

[essandess (Steve Smith)]

Something like the following tests whether mp-clang-3.9 is set to be the compiler, and avoids the issues of having to change macports.conf whenever clang is upgraded.

port select --show clang | perl -ne "chomp; s/The currently selected version for 'clang' is '(.*)'./\$1/; print $_;"

[mamoll (Mark Moll)]

We can add clang38/clang39 variants:

variant clang38 description "Use clang-3.8 and enable OpenMP" conflicts clang39 {
      configure.compiler  macports-clang-3.8
}

variant clang38 description "Use clang-3.9 and enable OpenMP" conflicts clang38 {
      configure.compiler  macports-clang-3.9
}

The next question is then do you think +clang38 should be a default variant?

[essandess (Steve Smith)]

Replying to mmoll@…:

We can add clang38/clang39 variants:

variant clang38 description "Use clang-3.8 and enable OpenMP" conflicts clang39 {
      configure.compiler  macports-clang-3.8
}

variant clang38 description "Use clang-3.9 and enable OpenMP" conflicts clang38 {
      configure.compiler  macports-clang-3.9
}

The next question is then do you think +clang38 should be a default variant?

Yes, variants are a great idea.

My personal preference would be default OpenMP support because multithreading makes my code scream on large graphs, and all my boxes have multiple cores anyway. I suspect this is common among graph-tool users, although I'd defer to Tiago or others who have experience with omp build robustness.

[essandess (Steve Smith)]

PS typo in the clang39 variant if you go that route.

[count0 (Tiago de Paula Peixoto)]

My personal preference would be default OpenMP support because multithreading makes my code scream on large graphs, and all my boxes have multiple cores anyway. I suspect this is common among graph-tool users, although I'd defer to Tiago or others who have experience with omp build robustness.

I always enable openmp with GCC, and it is the default on all the packages I maintain (Debian/Ubuntu and Arch). Assuming the clang implementation is stable (I have no idea), it should be the default.

[essandess (Steve Smith)]

Rather than a "clang39" variant, I'd suggest an "openmp" variant that would specify whatever the latest clang version is and pass configure.args-append=--enable-openmp. And make this variant the default as Tiago says.

[mamoll (Mark Moll)]

Fixed in r147229.