Comments (25)
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I tried with Takis's docker image, it gets past the parwind crash, but then it errors out later in scribe_io.F90
:
At line 208 of file /app/schism/src/Core/scribe_io.F90
Fortran runtime error: Attempting to allocate already allocated variable 'iwork3'
Error termination. Backtrace:
At line 208 of file /app/schism/src/Core/scribe_io.F90
Fortran runtime error: Attempting to allocate already allocated variable 'iwork3'
Error termination. Backtrace:
At line 208 of file /app/schism/src/Core/scribe_io.F90
Fortran runtime error: Attempting to allocate already allocated variable 'iwork3'
Error termination. Backtrace:
At line 208 of file /app/schism/src/Core/scribe_io.F90
Fortran runtime error: Attempting to allocate already allocated variable 'iwork3'
Error termination. Backtrace:
#0 0x7f0d5bb94171 in ???
#1 0x7f0d5bb94d19 in ???
#2 0x7f0d5bb950fb in ???
#3 0x433de6 in ???
#4 0x404ed7 in ???
#5 0x404dd1 in ???
#6 0x405146 in ???
#7 0x405182 in ???
#8 0x7f0d5a189ca2 in ???
#9 0x404cfd in ???
#10 0xffffffffffffffff in ???
#0 0x7f196fa2e171 in ???
#1 0x7f196fa2ed19 in ???
#2 0x7f196fa2f0fb in ???
#0 0x7f28b0704171 in ???
#1 0x7f28b0704d19 in ???
#2 0x7f28b07050fb in ???
#3 0x433de6 in ???
#4 0x404ed7 in ???
#5 0x404dd1 in ???
.
.
.
#10 0xffffffffffffffff in ???
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
[a2f80da41728:00204] *** An error occurred in MPI_Send
[a2f80da41728:00204] *** reported by process [3351379969,2]
[a2f80da41728:00204] *** on communicator MPI COMMUNICATOR 3 DUP FROM 0
[a2f80da41728:00204] *** MPI_ERR_OTHER: known error not in list
[a2f80da41728:00204] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
[a2f80da41728:00204] *** and potentially your MPI job)
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[51138,1],7]
Exit code: 2
--------------------------------------------------------------------------
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This is a new container (with different gcc and netcdf,etc version) that gave me this new error, I haven't tested this with nws=0
but in my older container, I did confirm that nws=0
was going through.
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In the case of the new container from Takis, I get the schism scribe_io
error even when nws
is equal to 0
. I'm using e2b943a
commit. But I think I saw the same thing with an earlier commit as well.
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Joseph hi,
I updated the PaHM sources in SCHISM. You might want to check the parwind.F90 file to see if the modifications are ok.
I have compiled and ran SCHISM+PAHM using GFortran/OpenMPI without issues now. It seems they were some memory
allocation conflicts with PaHM.
The flags I used to compile SCHISM with GFortran are:
cmake ../src/ -DCMAKE_Fortran_COMPILER=mpifort -DCMAKE_C_COMPILER=mpicc -DNetCDF_Fortran_LIBRARY=$(nc-config --libdir)
/libnetcdff.so -DNetCDF_C_LIBRARY=$(nc-config --libdir)
/libnetcdf.so -DNetCDF_INCLUDE_DIR=$(nc-config --includedir)
-DUSE_PAHM=TRUE -DCMAKE_Fortran_FLAGS_RELEASE="-O2 -ffree-line-length-none -fallow-argument-mismatch"
For debugging I used:
cmake ../src/ -DCMAKE_Fortran_COMPILER=mpifort -DCMAKE_C_COMPILER=mpicc -DNetCDF_Fortran_LIBRARY=$(nc-config --libdir)
/libnetcdff.so -DNetCDF_C_LIBRARY=$(nc-config --libdir)
/libnetcdf.so -DNetCDF_INCLUDE_DIR=$(nc-config --includedir)
-DUSE_PAHM=TRUE -DCMAKE_Fortran_FLAGS_RELEASE="-O2 -ggdb -ffree-line-length-none -fallow-argument-mismatch -fallow-invalid-boz -fbacktrace -fno-range-check -fno-unsafe-math-optimizations -frounding-math -fsignaling-nans -ffpe-trap=invalid,zero,overflow -mcmodel=medium -march=k8 -m64 -Wall -Wline-truncation -Wcharacter-truncation -Wsurprising -Waliasing"
NOTICE: If I use -O0 in debugging mode, GFortran issues a segmentation fault due to the creation of temporary arrays
in the call in line 3920 of src/Hydro/schism_init.F90. You might want to check this piece of code.
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Just for future reference, this ticket is going to be fixed by #75
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@josephzhang8, I tested the updates in my container with GNU compiler and it doesn't crash anymore during reading hurricane track. I think we can move forward with merging this from the testing perspective
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shinnecock_sandy2012.zip
@josephzhang8 @pvelissariou1 this is a test case for Shinnecock mesh with parametric wind and tidal setup. I didn't validate anything since there are no stations here, but I know it runs successfully. This can potentially be included in SCHISM regression tests with GNU compilers to make sure PaHM-SCHISM works.
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@pvelissariou1, do you have any suggestions on the best way to validate this run? There are not COOPS stations to compare against within the Shinnecock mesh.
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I talked with @pvelissariou1. There used to be a station in that area for hurricane Sandy, I'll update the setup with that station location and we'll validate the water-level base on it
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When I check the data inventory for the inlet station it shows that only data for a brief period in late 2013 and early 2014 is available. I need to ask around and see how to validate given that data is not available from COOPS website.
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