I finally pinned down the actual cause of these regression in parallel builds on 10.11 with make 4.1 The issue was being triggered by the default usage of --enable-nls in the build. This drags in a libintl which is built against the CoreFoundation framework on darwin. The regressions on 10.11 can be either suppressed by building make 4.1 with the --disable-nls option or rebuilding gettext using the....

        gt_cv_func_CFPreferencesCopyAppValue=no \
        gt_cv_func_CFLocaleCopyCurrent=no \
        gt_cv_func_CFPreferencesCopyAppValue=no \
        gt_cv_func_CFLocaleCopyCurrent=no

in order to prevent linkage of libintl against the CoreFoundation framework. This also corresponds with the known behavior of pymol which uses fork()/exec() under tcl. On darwin, tcl has to be built with --disable-corefoundation to avoid crashes in pymol. Looking at the CoreFoundation framework sources, there doesn't appear to be any effort to handle EINTR error codes on read(), write() and (f)stat() calls.

I finally puzzled out that this regression in the builds of gcc 5.2.0 and openmpi can be suppressed by rebuilding make 4.1 with --disable-nls. This actually makes sense as there seems to be be incomplete usage of the nonintr_read and nonintr_write calls that check for EINTR in gettext-0.19.5.1/gettext-tools/gnulib-lib. Also I don't see any matching nonintr_stat/nonintr_fstat calls in gettext-0.19.5.1/gettext-tools/gnulib-lib or checks for EINTR when stat()/fstat() is used there.

using

EINTRLOOP(job_rfd, dup (job_fds[0]));

instead of

job_rfd = dup (job_fds[0]);

in the new_job() subroutine of job.c results in a  hang during the parallel build of gcc 5.2.0 rather than the previous error...

make[5]: * read jobs pipe: No such file or directory. Stop.

The full error that we are seeing on OS X 10.11 under make 4.1 called from perl after a flock() is...

make[5]: * read jobs pipe: No such file or directory.  Stop.
make[5]: * Waiting for unfinished jobs....
libtool: compile:  /sw/src/fink.build/gcc5-5.2.0-2/darwin_objdir/./gcc/gcj -B/sw/src/fink.build/gcc5-5.2.0-2/darwin_objdir/x86_64-apple-darwin15.0.0/i386/libjava/ -B/sw/src/fink.build/gcc5-5.2.0-2/darwin_objdir/x86_64-apple-darwin15.0.0/i386/libjava/ -B/sw/src/fink.build/gcc5-5.2.0-2/darwin_objdir/./gcc/ -B/sw/lib/gcc5/x86_64-apple-darwin15.0.0/bin/ -B/sw/lib/gcc5/x86_64-apple-darwin15.0.0/lib/ -isystem /sw/lib/gcc5/x86_64-apple-darwin15.0.0/include -isystem /sw/lib/gcc5/x86_64-apple-darwin15.0.0/sys-include -m32 -ffloat-store -fomit-frame-pointer -Usun -fclasspath= -fbootclasspath=../../../../gcc-5.2.0/libjava/classpath/lib --encoding=UTF-8 -Wno-deprecated -fbootstrap-classes -g -O2 -m32 -c --resource gnu/java/locale/LocaleInformation_gaa.properties ../../../../gcc-5.2.0/libjava/classpath/resource/gnu/java/locale/LocaleInformation_gaa.properties  -fno-common -o gnu/java/locale/.libs/LocaleInformation_gaa.properties.o
Makefile:10240: recipe for target 'all-recursive' failed
make[4]: * [all-recursive] Error 1
make[4]: Leaving directory '/sw/src/fink.build/gcc5-5.2.0-2/darwin_objdir/x86_64-apple-darwin15.0.0/i386/libjava'
Makefile:12804: recipe for target 'multi-do' failed
make[3]: * [multi-do] Error 1
make[3]: Leaving directory '/sw/src/fink.build/gcc5-5.2.0-2/darwin_objdir/x86_64-apple-darwin15.0.0/libjava'
Makefile:12768: recipe for target 'all-multi' failed
make[2]: * [all-multi] Error 2
make[2]: Leaving directory '/sw/src/fink.build/gcc5-5.2.0-2/darwin_objdir/x86_64-apple-darwin15.0.0/libjava'
Makefile:17475: recipe for target 'all-target-libjava' failed
make[1]: * [all-target-libjava] Error 2
Makefile:21086: recipe for target 'bootstrap-lean' failed
make: * [bootstrap-lean] Error 141
make: INTERNAL: Exiting with 1 jobserver tokens available; should be 8!

in the parallel make  FSF gcc 5.2.0 build. My understanding is that the error code 141 is an error above 128 indicating a termination due to signal which in this case would be 141-128=13 or "Broken pipe: write to pipe with no readers".

There seems to still be missing EINTRLOOP () macro usage on OS X 10.11. The gcc 5.2.0 parallel build still fails but the initial error in its case is...

make[5]: * read jobs pipe: No such file or directory.  Stop.

...ending with...

make: INTERNAL: Exiting with 1 jobserver tokens available; should be 8!

so I am guessing we need a EINTRLOOP  wrapper on...

got_token = read (job_rfd, &token, 1);

in new_job() of job.c as well.

The change...

diff -uNr make-4.1.orig/main.c make-4.1/main.c
--- make-4.1.orig/main.c        2014-10-05 12:24:51.000000000 -0400
+++ make-4.1/main.c     2015-10-20 22:08:00.000000000 -0400
@@ -3364,9 +3364,12 @@
 #else
       /* Close the write side, so the read() won't hang.  */
       close (job_fds[1]);
-
-      while (read (job_fds[0], &token, 1) == 1)
+      int r;
+      EINTRLOOP (r, read (job_fds[0], &token, 1));
+      while (r == 1) {
         ++tcnt;
+       EINTRLOOP (r, read (job_fds[0], &token, 1));
+      }
 #endif
 
       if (tcnt != master_job_slots)

seems to eliminate the failures here on OS X 10.12.