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soedinglab / tejaas

Tejaas - a tool for discovering trans-eQTLs
https://github.com/soedinglab/tejaas/wiki
GNU General Public License v3.0
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SystemError when gathering I x G p-values #1

Closed banskt closed 6 years ago

banskt commented 6 years ago

Traceback error message:

Traceback (most recent call last):
  File "codebase/tejaas/bin/../main.py", line 65, in <module>
    jpa.compute()
  File "/home/mpg08/sbanerj/trans-eQTL/codebase/tejaas/qstats/jpa.py", line 118, in compute
    self.mpicompute()
  File "/home/mpg08/sbanerj/trans-eQTL/codebase/tejaas/qstats/jpa.py", line 104, in mpicompute
    pvals   = self.comm.gather(pvals,   root = 0)
  File "MPI/Comm.pyx", line 1281, in mpi4py.MPI.Comm.gather (src/mpi4py.MPI.c:108949)
  File "MPI/msgpickle.pxi", line 664, in mpi4py.MPI.PyMPI_gather (src/mpi4py.MPI.c:47643)
  File "MPI/msgpickle.pxi", line 179, in mpi4py.MPI.Pickle.allocv (src/mpi4py.MPI.c:41800)
  File "MPI/msgpickle.pxi", line 127, in mpi4py.MPI.Pickle.alloc (src/mpi4py.MPI.c:40945)
SystemError: Negative size passed to PyBytes_FromStringAndSize
banskt commented 6 years ago

Likely a 32-bits overflow. Probable solution

timkartar commented 6 years ago

I already found it and was working on it. Although looks like nothing to work on anymore :-)

On Mon, Jun 18, 2018 at 8:21 PM, Saikat Banerjee notifications@github.com wrote:

Likely a 32-bits overflow. Probable solution https://groups.google.com/forum/#!topic/mpi4py/r95uGPcqXLA

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