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Fix segfault on restart read? #30

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Fix segfault on restart read? #30

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7 changes: 4 additions & 3 deletions core/io.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1519,6 +1519,7 @@ void restart_read(char *fname) {
nph_in += dset_sizes[n];
}
H5Sclose(space);
H5Dclose(ph_dsets[n]);
}
printf("[%i] nph_in = %lu\n", mpi_myrank(), (unsigned long int)nph_in);
// Actually read datasets
Expand All @@ -1527,8 +1528,11 @@ void restart_read(char *fname) {
int noffset = 0;
for (int n = 0; n < num_datasets; n++) {
if (n % mpi_nprocs() == mpi_myrank()) {
sprintf(dsetnam, "photons_%08d", n);
ph_dsets[n] = H5Dopen(file_id, dsetnam, H5P_DEFAULT);
H5Dread(ph_dsets[n], phmemtype, H5S_ALL, H5S_ALL, H5P_DEFAULT,
&rdata[noffset]);
H5Dclose(ph_dsets[n]);
noffset += dset_sizes[n];
}
}
Expand Down Expand Up @@ -1573,9 +1577,6 @@ void restart_read(char *fname) {
}

free(rdata);
for (int n = 0; n < num_datasets; n++) {
H5Dclose(ph_dsets[n]);
}
free(ph_dsets);
free(dset_sizes);
#endif // RADIATION
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3 changes: 2 additions & 1 deletion script/machine/debian.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,8 @@ def get_options():
host = {}

host['NAME'] = os.uname()[1]
host['COMPILER'] = '/usr/local/hdf5-parallel/bin/h5pcc'
#host['COMPILER'] = '/usr/local/hdf5-parallel/bin/h5pcc'
host['COMPILER'] = 'h5pcc'
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Should not be merged like this... but my vm is named ubuntu but my h5pcc isn't at this path. Maybe the solution is turning host['COMPILER'] into an array of strings all of which are searched?

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I don't think I want to do a "search" thing. I think these machine files are intended to be modified... and debian was just a template.

host['COMPILER_FLAGS'] = flags_base + ' ' + fcflags + ' ' + '-O2 -march=native'
host['DEBUG_FLAGS'] = flags_base + ' ' + fcflags + ' ' + '-g -O0'
host['GSL_DIR'] = ''
Expand Down