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vscentrum / vsc-software-stack

Central repository of easyconfigs used in the software installations on VSC clusters.
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Sagemath + plantri #253

Open laraPPr opened 7 months ago

laraPPr commented 7 months ago
PetrKralCZ commented 4 months ago
PetrKralCZ commented 1 month ago
PetrKralCZ commented 1 month ago
PetrKralCZ commented 1 month ago
PetrKralCZ commented 1 month ago
PetrKralCZ commented 1 month ago
PetrKralCZ commented 1 month ago
PetrKralCZ commented 1 month ago
PetrKralCZ commented 1 month ago
boegel commented 4 weeks ago

@PetrKralCZ You mentioned that the Sagemath installation currently fails with:

      error: command '/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/13.2.0/bin/gcc' failed with exit code 1
      Exception ignored in: <function Pool.__del__ at 0x1481e0e2a2a0>
      Traceback (most recent call last):
        File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.5-GCCcore-13.2.0/lib/python3.11/multiprocessing/pool.py", line 271, in __del__
          self._change_notifier.put(None)
        File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.5-GCCcore-13.2.0/lib/python3.11/multiprocessing/queues.py", line 377, in put
          self._writer.send_bytes(obj)
        File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.5-GCCcore-13.2.0/lib/python3.11/multiprocessing/connection.py", line 199, in send_bytes
          self._send_bytes(m[offset:offset + size])
        File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.5-GCCcore-13.2.0/lib/python3.11/multiprocessing/connection.py", line 410, in _send_bytes
          self._send(header + buf)
        File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.5-GCCcore-13.2.0/lib/python3.11/multiprocessing/connection.py", line 367, in _send
          n = write(self._handle, buf)
              ^^^^^^^^^^^^^^^^^^^^^^^^
      OSError: [Errno 9] Bad file descriptor
      [end of output]

From the log you provided, it seems like the actual compiler error is this though:

      build/cythonized/sage/rings/polynomial/pbori/pbori.cpp:1253:10: fatal error: polybori/pbori_defs.h: No such file or directory
       1253 | #include "polybori/pbori_defs.h"
            |          ^~~~~~~~~~~~~~~~~~~~~~~
      compilation terminated.

The OSError above is probably fallout from the gcc compilation command failing.