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schism-dev / schism

Semi-implicit Cross-scale Hydroscience Integrated System Model (SCHISM)
http://ccrm.vims.edu/schismweb/
Apache License 2.0
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NWS = -1 crash with GNU compiler #73

Open SorooshMani-NOAA opened 2 years ago

SorooshMani-NOAA commented 2 years ago

Related to https://github.com/noaa-ocs-modeling/PaHM/issues/8

In my workflow I use SCHISM compiled in a Docker image. I'm using GNU compilers on ubuntu for the image. Recently after rebuilding, I noticed a crash when nws=-1. The crash won't happen if I just set nws=0 for the same set of input files. Also when I compile using intel/2021.3.0 I don't see the crash for the exact same input files.

This setup (Docker + GNU) used to work for me. I guess an update in GNU compilers or one of the libraries since the last time I built the image might be the reason behind this issue. (I don't fix the compiler or library versions in that docker image, I just install them using apt)

The details of the trackback can be found in the issue referred to at the top.

josephzhang8 commented 2 years ago

Hi Soroosh, Takis:

I tested it on gcc and also got a crash from parwind:

0: ABORT: Only "BEST", "OFCL", or "CALM" are allowed in the 5th column of hurricane-track.dat

It seems gcc failed to skip the empty field in the input hurricane-track.dat:

AL, 18, 2012102118, , BEST, 0, 143N,

This is related to the csv reader in PaHM but I'm not familiar with the details.

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Soroosh Mani @.> Sent: Tuesday, June 14, 2022 4:09 PM To: schism-dev/schism @.> Cc: Subscribed @.***> Subject: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue #73)

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Related to noaa-ocs-modeling/PaHM#8https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnoaa-ocs-modeling%2FPaHM%2Fissues%2F8&data=05%7C01%7Cyjzhang%40vims.edu%7Cb9c9cf9e5d294bddc4ec08da4e41c536%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637908341637758947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=I2xDecF%2BxzQD7dyH8Vb63m9eaGDO0Yeyf7WMNWKYVr8%3D&reserved=0

In my workflow I use SCHISM compiled in a Docker image. I'm using GNU compilers on ubuntu for the image. Recently after rebuilding, I noticed a crash when nws=-1. The crash won't happen if I just set nws=0 for the same set of input files. Also when I compile using intel/2021.3.0 I don't see the crash for the exact same input files.

This setup (Docker + GNU) used to work for me. I guess an update in GNU compilers or one of the libraries since the last time I built the image might be the reason behind this issue. (I don't fix the compiler or library versions in that docker image, I just install them using apt)

The details of the trackback can be found in the issue referred to at the top.

- Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fschism-dev%2Fschism%2Fissues%2F73&data=05%7C01%7Cyjzhang%40vims.edu%7Cb9c9cf9e5d294bddc4ec08da4e41c536%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637908341637758947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=IyLxzN6EXhkUmhXYgJjx1hRyq5GJ1RW5mlxuTVmgNrk%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAFBKNZ6PFQEXAHTOW32NGYTVPDRHBANCNFSM5YY5NZEQ&data=05%7C01%7Cyjzhang%40vims.edu%7Cb9c9cf9e5d294bddc4ec08da4e41c536%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637908341637758947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=rX%2ByyTmAQDXuU17%2FHV%2B56fnzLS2byHRI4p9F9nmWlmA%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.**@.>>

josephzhang8 commented 2 years ago

Dear Joseph,

Thank you for the reply. What version of gfortran are you using? Soroosh, will use my container to run schism with gfortran 8.3. Let's see if this is a gfortran issue first. We can switch reading the best track file using the old way (formatted input) If this is a gfortran issue, then most likely the bug is in the csv module. Let's wait for Soroosh; I'll do similar runs as well and I'll report back.

Takis

Panagiotis Velissariou, Ph.D., P.E. UCAR Scientist National Ocean and Atmospheric Administration National Ocean Service Office of Coast Survey CSDL/CMMB Project Lead - Coastal Coupling cell: (205) 227-9141 email: @.***

On Fri, Jun 17, 2022 at 12:20 PM Y. Joseph Zhang @.***> wrote:

Hi Soroosh, Takis:

I tested it on gcc and also got a crash from parwind:

0: ABORT: Only "BEST", "OFCL", or "CALM" are allowed in the 5th column of hurricane-track.dat

It seems gcc failed to skip the empty field in the input hurricane-track.dat:

AL, 18, 2012102118, , BEST, 0, 143N,

This is related to the csv reader in PaHM but I’m not familiar with the details.

-Joseph

Joseph Zhang

Office: (804) 684 7466

Web: schism.wiki

From: Soroosh Mani @.> Sent: Tuesday, June 14, 2022 4:09 PM To: schism-dev/schism @.> Cc: Subscribed @.**> Subject:* [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue

73)

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Related to noaa-ocs-modeling/PaHM#8 https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnoaa-ocs-modeling%2FPaHM%2Fissues%2F8&data=05%7C01%7Cyjzhang%40vims.edu%7Cb9c9cf9e5d294bddc4ec08da4e41c536%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637908341637758947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=I2xDecF%2BxzQD7dyH8Vb63m9eaGDO0Yeyf7WMNWKYVr8%3D&reserved=0

In my workflow I use SCHISM compiled in a Docker image. I'm using GNU compilers on ubuntu for the image. Recently after rebuilding, I noticed a crash when nws=-1. The crash won't happen if I just set nws=0 for the same set of input files. Also when I compile using intel/2021.3.0 I don't see the crash for the exact same input files.

This setup (Docker + GNU) used to work for me. I guess an update in GNU compilers or one of the libraries since the last time I built the image might be the reason behind this issue. (I don't fix the compiler or library versions in that docker image, I just install them using apt)

The details of the trackback can be found in the issue referred to at the top.

— Reply to this email directly, view it on GitHub https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fschism-dev%2Fschism%2Fissues%2F73&data=05%7C01%7Cyjzhang%40vims.edu%7Cb9c9cf9e5d294bddc4ec08da4e41c536%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637908341637758947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=IyLxzN6EXhkUmhXYgJjx1hRyq5GJ1RW5mlxuTVmgNrk%3D&reserved=0, or unsubscribe https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAFBKNZ6PFQEXAHTOW32NGYTVPDRHBANCNFSM5YY5NZEQ&data=05%7C01%7Cyjzhang%40vims.edu%7Cb9c9cf9e5d294bddc4ec08da4e41c536%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637908341637758947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=rX%2ByyTmAQDXuU17%2FHV%2B56fnzLS2byHRI4p9F9nmWlmA%3D&reserved=0 . You are receiving this because you are subscribed to this thread.Message ID: @.***>

josephzhang8 commented 2 years ago

See below. It's a latest gcc (on a new German AMD cluster Levante).

Currently Loaded Modulefiles: 1) python3/2022.01-gcc-11.2.0 3) gcc/11.2.0-gcc-11.2.0 5) netcdf-c/4.8.1-gcc-11.2.0 2) git/2.31.1-gcc-11.2.0 4) openmpi/4.1.2-gcc-11.2.0 6) netcdf-fortran/4.5.3-openmpi-4.1.2-gcc-11.2.0

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Panagiotis Velissariou - NOAA Affiliate @.> Sent: Friday, June 17, 2022 1:30 PM To: Y. Joseph Zhang @.> Cc: schism-dev/schism @.>; schism-dev/schism @.>; Subscribed @.>; Saeed Moghimi - NOAA Federal @.> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue #73)

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Dear Joseph,

Thank you for the reply. What version of gfortran are you using? Soroosh, will use my container to run schism with gfortran 8.3. Let's see if this is a gfortran issue first. We can switch reading the best track file using the old way (formatted input) If this is a gfortran issue, then most likely the bug is in the csv module. Let's wait for Soroosh; I'll do similar runs as well and I'll report back.

Takis

Panagiotis Velissariou, Ph.D., P.E. UCAR Scientist National Ocean and Atmospheric Administration National Ocean Service Office of Coast Survey CSDL/CMMB Project Lead - Coastal Coupling cell: (205) 227-9141 email: @.**@.>

On Fri, Jun 17, 2022 at 12:20 PM Y. Joseph Zhang @.**@.>> wrote: Hi Soroosh, Takis:

I tested it on gcc and also got a crash from parwind:

0: ABORT: Only "BEST", "OFCL", or "CALM" are allowed in the 5th column of hurricane-track.dat

It seems gcc failed to skip the empty field in the input hurricane-track.dat:

AL, 18, 2012102118, , BEST, 0, 143N,

This is related to the csv reader in PaHM but I'm not familiar with the details.

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Soroosh Mani @.**@.>> Sent: Tuesday, June 14, 2022 4:09 PM To: schism-dev/schism @.**@.>> Cc: Subscribed @.**@.>> Subject: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue #73)

[EXTERNAL to VIMS received message]

Related to noaa-ocs-modeling/PaHM#8https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnoaa-ocs-modeling%2FPaHM%2Fissues%2F8&data=05%7C01%7Cyjzhang%40vims.edu%7C8cef568339704004263908da50871abd%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637910838459752665%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gUq0nJ6XeRgq3ddNzUqQR43Xpdh%2BXoM5J0FumQM%2Bl9M%3D&reserved=0

In my workflow I use SCHISM compiled in a Docker image. I'm using GNU compilers on ubuntu for the image. Recently after rebuilding, I noticed a crash when nws=-1. The crash won't happen if I just set nws=0 for the same set of input files. Also when I compile using intel/2021.3.0 I don't see the crash for the exact same input files.

This setup (Docker + GNU) used to work for me. I guess an update in GNU compilers or one of the libraries since the last time I built the image might be the reason behind this issue. (I don't fix the compiler or library versions in that docker image, I just install them using apt)

The details of the trackback can be found in the issue referred to at the top.

- Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fschism-dev%2Fschism%2Fissues%2F73&data=05%7C01%7Cyjzhang%40vims.edu%7C8cef568339704004263908da50871abd%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637910838459908881%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=D%2BDOSO6JCsZeLhx3lglgcJXCkLZ4oyygoMq9lmgn%2F3Y%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAFBKNZ6PFQEXAHTOW32NGYTVPDRHBANCNFSM5YY5NZEQ&data=05%7C01%7Cyjzhang%40vims.edu%7C8cef568339704004263908da50871abd%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637910838459908881%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ri0OgAClqQ5CHnKSeXKuj4qY3gwN03MeHkX7KgKH9T8%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.**@.>>

SorooshMani-NOAA commented 2 years ago

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
--------------------------------------------------------------------------
josephzhang8 commented 2 years ago

Thx Soroosh. That error is strange as iwork3() is a local allocatable array that is allocated inside and deallocated after use. The MPI_send error below looks suspicious also. Another possibility is that some errors from PaHM did not cause crash immediately with gcc and then spilt over. I recall you said it's fine with nws /=-1.

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Soroosh Mani @.> Sent: Friday, June 17, 2022 2:53 PM To: schism-dev/schism @.> Cc: Y. Joseph Zhang @.>; Comment @.> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue #73)

[EXTERNAL to VIMS received message]

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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SorooshMani-NOAA commented 2 years ago

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.

SorooshMani-NOAA commented 2 years ago

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.

josephzhang8 commented 2 years ago

Strange indeed. I couldn't reproduce that on Levante - the run went fine with nws/= -1

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Soroosh Mani @.> Sent: Friday, June 17, 2022 4:01 PM To: schism-dev/schism @.> Cc: Y. Joseph Zhang @.>; Comment @.> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue #73)

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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

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pvelissariou1 commented 1 year ago

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.

josephzhang8 commented 1 year ago

Thank you Takis for working on this. I did a first round of review on your changes. My changes to PaHM were marked as 'YJZ' so I looked at those places in particular.

  1. In PaHM_Utilities.F90, I made a remark on a potential bug:

!YJZ error: lat0 in degrees x = DEG2RAD REARTH (lon - lon0) COS(lat0) y = DEG2RAD REARTH * lat

  1. Thx for the fix for _assert.F90.
  2. parwind: I see a lot of changes due to version differences. I'll need to spend some time going thru all of them, but can u or Soroosh please start testing to see if there are issues?

Thx.

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Panagiotis Velissariou @.> Sent: Tuesday, July 19, 2022 5:50 PM To: schism-dev/schism @.> Cc: Y. Joseph Zhang @.>; Comment @.> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue #73)

[EXTERNAL to VIMS received message]

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.

- Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fschism-dev%2Fschism%2Fissues%2F73%23issuecomment-1189584277&data=05%7C01%7Cyjzhang%40vims.edu%7C92fcdd9298494332db9808da69d09925%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637938641899647659%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=HD7NucfdiI1Cx7H5lJf7V1bVmLKVLTbBNV2RlYcCbIM%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAFBKNZ53YFVUK2UMIFBNPOLVU4PHNANCNFSM5YY5NZEQ&data=05%7C01%7Cyjzhang%40vims.edu%7C92fcdd9298494332db9808da69d09925%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637938641899647659%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mPmnIMsfkzASbjl4ZDUJ%2FNKtzi4MTxYrypvEWbcXaqg%3D&reserved=0. You are receiving this because you commented.Message ID: @.**@.>>

SorooshMani-NOAA commented 1 year ago

Just for future reference, this ticket is going to be fixed by #75

pvelissariou1 commented 1 year ago

Hi Joseph,

I did test it, run a test case and I didn't encounter any issues so far. I'll check it out: !YJZ error: lat0 in degrees x = DEG2RAD REARTH (lon - lon0) COS(lat0) y = DEG2RAD REARTH * lat

Takis

Panagiotis Velissariou, Ph.D., P.E. UCAR Scientist National Ocean and Atmospheric Administration National Ocean Service Office of Coast Survey CSDL/CMMB Project Lead - Coastal Coupling cell: (205) 227-9141 email: @.***

On Wed, Jul 20, 2022 at 7:39 AM Joseph Zhang @.***> wrote:

Thank you Takis for working on this. I did a first round of review on your changes. My changes to PaHM were marked as 'YJZ' so I looked at those places in particular.

  1. In PaHM_Utilities.F90, I made a remark on a potential bug:

!YJZ error: lat0 in degrees x = DEG2RAD REARTH (lon - lon0) COS(lat0) y = DEG2RAD REARTH * lat

  1. Thx for the fix for _assert.F90.
  2. parwind: I see a lot of changes due to version differences. I'll need to spend some time going thru all of them, but can u or Soroosh please start testing to see if there are issues?

Thx.

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Panagiotis Velissariou @.> Sent: Tuesday, July 19, 2022 5:50 PM To: schism-dev/schism @.> Cc: Y. Joseph Zhang @.>; Comment @.> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue

73)

[EXTERNAL to VIMS received message]

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.

- Reply to this email directly, view it on GitHub< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fschism-dev%2Fschism%2Fissues%2F73%23issuecomment-1189584277&data=05%7C01%7Cyjzhang%40vims.edu%7C92fcdd9298494332db9808da69d09925%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637938641899647659%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=HD7NucfdiI1Cx7H5lJf7V1bVmLKVLTbBNV2RlYcCbIM%3D&reserved=0>, or unsubscribe< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAFBKNZ53YFVUK2UMIFBNPOLVU4PHNANCNFSM5YY5NZEQ&data=05%7C01%7Cyjzhang%40vims.edu%7C92fcdd9298494332db9808da69d09925%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637938641899647659%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mPmnIMsfkzASbjl4ZDUJ%2FNKtzi4MTxYrypvEWbcXaqg%3D&reserved=0

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pvelissariou1 commented 1 year ago

I fixed the bug in: x = DEG2RAD REARTH (lon - lon0) COS(lat0) as x = DEG2RAD REARTH (lon - lon0) COS(REARTH * lat0)

This was in two places in PaHM_Utilities.F90 Thank you Joseph for pointing this out. I don't understand how I missed it.

Takis

Panagiotis Velissariou, Ph.D., P.E. UCAR Scientist National Ocean and Atmospheric Administration National Ocean Service Office of Coast Survey CSDL/CMMB Project Lead - Coastal Coupling cell: (205) 227-9141 email: @.***

On Wed, Jul 20, 2022 at 7:39 AM Joseph Zhang @.***> wrote:

Thank you Takis for working on this. I did a first round of review on your changes. My changes to PaHM were marked as 'YJZ' so I looked at those places in particular.

  1. In PaHM_Utilities.F90, I made a remark on a potential bug:

!YJZ error: lat0 in degrees x = DEG2RAD REARTH (lon - lon0) COS(lat0) y = DEG2RAD REARTH * lat

  1. Thx for the fix for _assert.F90.
  2. parwind: I see a lot of changes due to version differences. I'll need to spend some time going thru all of them, but can u or Soroosh please start testing to see if there are issues?

Thx.

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Panagiotis Velissariou @.> Sent: Tuesday, July 19, 2022 5:50 PM To: schism-dev/schism @.> Cc: Y. Joseph Zhang @.>; Comment @.> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue

73)

[EXTERNAL to VIMS received message]

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.

- Reply to this email directly, view it on GitHub< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fschism-dev%2Fschism%2Fissues%2F73%23issuecomment-1189584277&data=05%7C01%7Cyjzhang%40vims.edu%7C92fcdd9298494332db9808da69d09925%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637938641899647659%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=HD7NucfdiI1Cx7H5lJf7V1bVmLKVLTbBNV2RlYcCbIM%3D&reserved=0>, or unsubscribe< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAFBKNZ53YFVUK2UMIFBNPOLVU4PHNANCNFSM5YY5NZEQ&data=05%7C01%7Cyjzhang%40vims.edu%7C92fcdd9298494332db9808da69d09925%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637938641899647659%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mPmnIMsfkzASbjl4ZDUJ%2FNKtzi4MTxYrypvEWbcXaqg%3D&reserved=0

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josephzhang8 commented 1 year ago

Thx Takis.

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Panagiotis Velissariou @.> Sent: Wednesday, July 20, 2022 12:57 PM To: schism-dev/schism @.> Cc: Y. Joseph Zhang @.>; Comment @.> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue #73)

[EXTERNAL to VIMS received message]

I fixed the bug in: x = DEG2RAD REARTH (lon - lon0) COS(lat0) as x = DEG2RAD REARTH (lon - lon0) COS(REARTH * lat0)

This was in two places in PaHM_Utilities.F90 Thank you Joseph for pointing this out. I don't understand how I missed it.

Takis

Panagiotis Velissariou, Ph.D., P.E. UCAR Scientist National Ocean and Atmospheric Administration National Ocean Service Office of Coast Survey CSDL/CMMB Project Lead - Coastal Coupling cell: (205) 227-9141 email: @.<mailto:@.>

On Wed, Jul 20, 2022 at 7:39 AM Joseph Zhang @.<mailto:@.>> wrote:

Thank you Takis for working on this. I did a first round of review on your changes. My changes to PaHM were marked as 'YJZ' so I looked at those places in particular.

  1. In PaHM_Utilities.F90, I made a remark on a potential bug:

!YJZ error: lat0 in degrees x = DEG2RAD REARTH (lon - lon0) COS(lat0) y = DEG2RAD REARTH * lat

  1. Thx for the fix for _assert.F90.
  2. parwind: I see a lot of changes due to version differences. I'll need to spend some time going thru all of them, but can u or Soroosh please start testing to see if there are issues?

Thx.

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Panagiotis Velissariou @.<mailto:@.>> Sent: Tuesday, July 19, 2022 5:50 PM To: schism-dev/schism @.<mailto:@.>> Cc: Y. Joseph Zhang @.<mailto:@.>>; Comment @.<mailto:@.>> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue

73)

[EXTERNAL to VIMS received message]

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.

- Reply to this email directly, view it on GitHub< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fschism-dev%2Fschism%2Fissues%2F73%23issuecomment-1189584277&data=05%7C01%7Cyjzhang%40vims.edu%7C92fcdd9298494332db9808da69d09925%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637938641899647659%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=HD7NucfdiI1Cx7H5lJf7V1bVmLKVLTbBNV2RlYcCbIM%3D&reserved=0>, or unsubscribe< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAFBKNZ53YFVUK2UMIFBNPOLVU4PHNANCNFSM5YY5NZEQ&data=05%7C01%7Cyjzhang%40vims.edu%7C92fcdd9298494332db9808da69d09925%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637938641899647659%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mPmnIMsfkzASbjl4ZDUJ%2FNKtzi4MTxYrypvEWbcXaqg%3D&reserved=0

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josephzhang8 commented 1 year ago

Hi Takis:

I'm done reviewing your changes in parwind.F90 (I don't think I changed anything for other files except _Utility). They look good; I only have 1 question:

On line 1156 etc, the uses of 'windReduction' seem inconsistent? i.e. sometimes '/' and other times '*'. Thx.

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Joseph Zhang @.> Sent: Wednesday, July 20, 2022 1:21 PM To: schism-dev/schism @.> Cc: Y. Joseph Zhang @.>; Your activity @.> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue #73)

[EXTERNAL to VIMS received message]

Thx Takis.

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Panagiotis Velissariou @.<mailto:@.>> Sent: Wednesday, July 20, 2022 12:57 PM To: schism-dev/schism @.<mailto:@.>> Cc: Y. Joseph Zhang @.<mailto:@.>>; Comment @.<mailto:@.>> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue #73)

[EXTERNAL to VIMS received message]

I fixed the bug in: x = DEG2RAD REARTH (lon - lon0) COS(lat0) as x = DEG2RAD REARTH (lon - lon0) COS(REARTH * lat0)

This was in two places in PaHM_Utilities.F90 Thank you Joseph for pointing this out. I don't understand how I missed it.

Takis

Panagiotis Velissariou, Ph.D., P.E. UCAR Scientist National Ocean and Atmospheric Administration National Ocean Service Office of Coast Survey CSDL/CMMB Project Lead - Coastal Coupling cell: (205) 227-9141 email: @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>

On Wed, Jul 20, 2022 at 7:39 AM Joseph Zhang @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> wrote:

Thank you Takis for working on this. I did a first round of review on your changes. My changes to PaHM were marked as 'YJZ' so I looked at those places in particular.

  1. In PaHM_Utilities.F90, I made a remark on a potential bug:

!YJZ error: lat0 in degrees x = DEG2RAD REARTH (lon - lon0) COS(lat0) y = DEG2RAD REARTH * lat

  1. Thx for the fix for _assert.F90.
  2. parwind: I see a lot of changes due to version differences. I'll need to spend some time going thru all of them, but can u or Soroosh please start testing to see if there are issues?

Thx.

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Panagiotis Velissariou @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> Sent: Tuesday, July 19, 2022 5:50 PM To: schism-dev/schism @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> Cc: Y. Joseph Zhang @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>; Comment @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue

73)

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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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SorooshMani-NOAA commented 1 year ago

@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

josephzhang8 commented 1 year ago

Very good; please continue the test. I'll accept Takis' PR and merge to master. Thx.

-Joseph

Y. Joseph Zhang Web: schism.wiki Office: 804 684 7466

From: Soroosh Mani @.> Sent: Thursday, July 21, 2022 10:16 AM To: schism-dev/schism @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue #73)

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@josephzhang8https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjosephzhang8&data=05%7C01%7Cyjzhang%40vims.edu%7C1c1e9d49876840cdecd508da6b237b52%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637940097383380650%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=MPpsG0cTxADvgxbXPumwB3u1PIWE%2BpyuFizvftDQ%2FMs%3D&reserved=0, 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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SorooshMani-NOAA commented 1 year ago

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.

josephzhang8 commented 1 year ago

Many thanks, Soroosh!

I've redone the run on our side, and looked at the results. They seem to make sense; in particular, the wind field did not start until Day ~7 or so b/c the hurricane is far away. The tidal vel seems correct also.

Before I upload it to svn test suite, can you or Takis do any round of checking to make sure the results are actually correct? I'll be happy to prepare plots if u tell me what to look at.

Thx.

-Joseph

Y. Joseph Zhang Web: schism.wiki Office: 804 684 7466

From: Soroosh Mani @.> Sent: Friday, July 22, 2022 2:14 PM To: schism-dev/schism @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue #73)

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SorooshMani-NOAA commented 1 year ago

@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.

SorooshMani-NOAA commented 1 year ago

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

SorooshMani-NOAA commented 1 year ago

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.

josephzhang8 commented 1 year ago

Thx Soroosh. If you cannot find any obs, we'll just generate some plots from the current run as 'benchmark'.

-Joseph

Y. Joseph Zhang Web: schism.wiki Office: 804 684 7466

From: Soroosh Mani @.> Sent: Monday, July 25, 2022 1:59 PM To: schism-dev/schism @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue #73)

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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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pvelissariou1 commented 1 year ago

Hi Joseph,

What happens is that the "windReduction" factor is used to convert the gradient level (top of the atmospheric boundary layer, ~1000 m above the surface) winds that the Holland model calculates to the 10-m winds that the models require, thus the multiplication by the "windReduction" in this case (lines 1156, 1157). On the other hand, the best track files report the wind data at 10-m above the surface, therefore we need to divide by the "windReduction" factor (line 1092); wind speed increases due to less or no friction at the level above the atmospheric boundary layer.

Takis

Panagiotis Velissariou, Ph.D., P.E. UCAR Scientist National Ocean and Atmospheric Administration National Ocean Service Office of Coast Survey CSDL/CMMB Project Lead - Coastal Coupling cell: (205) 227-9141 email: @.***

On Wed, Jul 20, 2022 at 2:15 PM Joseph Zhang @.***> wrote:

Hi Takis:

I'm done reviewing your changes in parwind.F90 (I don't think I changed anything for other files except _Utility). They look good; I only have 1 question:

On line 1156 etc, the uses of 'windReduction' seem inconsistent? i.e. sometimes '/' and other times '*'. Thx.

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Joseph Zhang @.> Sent: Wednesday, July 20, 2022 1:21 PM To: schism-dev/schism @.> Cc: Y. Joseph Zhang @.>; Your activity @.> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue

73)

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Thx Takis.

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Panagiotis Velissariou @.<mailto:@.>> Sent: Wednesday, July 20, 2022 12:57 PM To: schism-dev/schism @.<mailto:@.>> Cc: Y. Joseph Zhang @.<mailto:@.>>; Comment @.<mailto:@.>> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue

73)

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I fixed the bug in: x = DEG2RAD REARTH (lon - lon0) COS(lat0) as x = DEG2RAD REARTH (lon - lon0) COS(REARTH * lat0)

This was in two places in PaHM_Utilities.F90 Thank you Joseph for pointing this out. I don't understand how I missed it.

Takis

Panagiotis Velissariou, Ph.D., P.E. UCAR Scientist National Ocean and Atmospheric Administration National Ocean Service Office of Coast Survey CSDL/CMMB Project Lead - Coastal Coupling cell: (205) 227-9141 email: @.<mailto:@.<mailto: @.%3cmailto:@.>>

On Wed, Jul 20, 2022 at 7:39 AM Joseph Zhang @.<mailto: @.mailto:***@***.***%3cmailto:***@***.***>> wrote:

Thank you Takis for working on this. I did a first round of review on your changes. My changes to PaHM were marked as 'YJZ' so I looked at those places in particular.

  1. In PaHM_Utilities.F90, I made a remark on a potential bug:

!YJZ error: lat0 in degrees x = DEG2RAD REARTH (lon - lon0) COS(lat0) y = DEG2RAD REARTH * lat

  1. Thx for the fix for _assert.F90.
  2. parwind: I see a lot of changes due to version differences. I'll need to spend some time going thru all of them, but can u or Soroosh please start testing to see if there are issues?

Thx.

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Panagiotis Velissariou @.<mailto:@.<mailto: @.%3cmailto:@.>>> Sent: Tuesday, July 19, 2022 5:50 PM To: schism-dev/schism @.<mailto:@.<mailto: @.%3cmailto:@.>>> Cc: Y. Joseph Zhang @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>; Comment @.<mailto:@.<mailto: @.%3cmailto:@.>>> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue

73)

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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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josephzhang8 commented 1 year ago

To qualify as regression test, we need to be able to assess future results against some 'standard' either qualitatively or quantitatively. I'll generate and save some plots but let me know if you want any metrics to be used. Thx.

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Joseph Zhang @.> Sent: Friday, July 22, 2022 5:42 PM To: schism-dev/schism @.> Cc: Y. Joseph Zhang @.>; Your activity @.> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue #73)

[EXTERNAL to VIMS received message]

Many thanks, Soroosh!

I've redone the run on our side, and looked at the results. They seem to make sense; in particular, the wind field did not start until Day ~7 or so b/c the hurricane is far away. The tidal vel seems correct also.

Before I upload it to svn test suite, can you or Takis do any round of checking to make sure the results are actually correct? I'll be happy to prepare plots if u tell me what to look at.

Thx.

-Joseph

Y. Joseph Zhang Web: schism.wiki Office: 804 684 7466

From: Soroosh Mani @.<mailto:@.>> Sent: Friday, July 22, 2022 2:14 PM To: schism-dev/schism @.<mailto:@.>> Cc: Y. Joseph Zhang @.<mailto:@.>>; Mention @.<mailto:@.>> Subject: Re: [schism-dev/schism] NWS = -1 crash with GNU compiler (Issue #73)

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