ERROR IN TGE DETERMINING ISONB

[asafaie]

While running FVCOM, I get the following error:
FVCOM Fatal Error!
ERROR IN TGE DETERMINING ISONB
Stopping FVCOM
Could you please help me to find the problem?
I have previously tested my mesh and input files in another linux machine and the model was working fine.

[Ricardo Torres]

Hi Looks like you still have a problem with the mesh or at least information related to the mesh. I am afraid I don’t have any specific advise beyond checking the mesh and setup again. Specially if you have upgraded to the latest fvcom recently. R From: asafaie [mailto:[e-mail]] Sent: 12 April 2020 21:38 To: pwcazenave/fvcom-toolbox Cc: Subscribed Subject: [pwcazenave/fvcom-toolbox] ERROR IN TGE DETERMINING ISONB (#11) While running FVCOM, I get the following error: FVCOM Fatal Error! ERROR IN TGE DETERMINING ISONB Stopping FVCOM Could you please help me to find the problem? I have previously tested my mesh and input files in another linux machine and the model was working fine. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#11>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABGHWPZGZWU7OLNGCDLGNFDRMIRAXANCNFSM4MGRTQKQ>.

…

________________________________ This email has been scanned by PML for spam & viruses. If you believe this email should have been stopped by our filters, click here<https://portal.mailanyone.net/index.html#/outer/reportspam?token=dXNlcj1yaXRvQHBtbC5hYy51azt0cz0xNTg2NzIzODU4O3V1aWQ9NUU5MzdDMTIwRUQxQTgxRTgyNkNBNTc0NTJFQjMwNzc7dG9rZW49MTlkM2I0N2ZjN2Y2YTRlMTNmMWM0MjMwZDVhYzc1Y2QxODJhMjE1MTs%3D> to report it. Please visit our new website at www.pml.ac.uk and follow us on Twitter @PlymouthMarine We have updated our Privacy Notice which is available at http://www.pml.ac.uk/System-pages/Privacy_Notice Plymouth Marine Laboratory (PML) is a company limited by guarantee registered in England & Wales, company number 4178503. Registered Charity No. 1091222. Registered Office: Prospect Place, The Hoe, Plymouth PL1 3DH, UK. This message is private and confidential. If you have received this message in error, please notify the sender and remove it from your system. You are reminded that e-mail communications are not secure and may contain viruses; PML accepts no liability for any loss or damage which may be caused by viruses.

[asafaie]

Hi Looks like you still have a problem with the mesh or at least information related to the mesh. I am afraid I don’t have any specific advise beyond checking the mesh and setup again. Specially if you have upgraded to the latest fvcom recently. R From: asafaie [mailto:[e-mail]] Sent: 12 April 2020 21:38 To: pwcazenave/fvcom-toolbox Cc: Subscribed Subject: [pwcazenave/fvcom-toolbox] ERROR IN TGE DETERMINING ISONB (#11) While running FVCOM, I get the following error: FVCOM Fatal Error! ERROR IN TGE DETERMINING ISONB Stopping FVCOM Could you please help me to find the problem? I have previously tested my mesh and input files in another linux machine and the model was working fine. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#11>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABGHWPZGZWU7OLNGCDLGNFDRMIRAXANCNFSM4MGRTQKQ.
…
________________________________ This email has been scanned by PML for spam & viruses. If you believe this email should have been stopped by our filters, click herehttps://portal.mailanyone.net/index.html#/outer/reportspam?token=dXNlcj1yaXRvQHBtbC5hYy51azt0cz0xNTg2NzIzODU4O3V1aWQ9NUU5MzdDMTIwRUQxQTgxRTgyNkNBNTc0NTJFQjMwNzc7dG9rZW49MTlkM2I0N2ZjN2Y2YTRlMTNmMWM0MjMwZDVhYzc1Y2QxODJhMjE1MTs%3D to report it. Please visit our new website at www.pml.ac.uk and follow us on Twitter @PlymouthMarine We have updated our Privacy Notice which is available at http://www.pml.ac.uk/System-pages/Privacy_Notice Plymouth Marine Laboratory (PML) is a company limited by guarantee registered in England & Wales, company number 4178503. Registered Charity No. 1091222. Registered Office: Prospect Place, The Hoe, Plymouth PL1 3DH, UK. This message is private and confidential. If you have received this message in error, please notify the sender and remove it from your system. You are reminded that e-mail communications are not secure and may contain viruses; PML accepts no liability for any loss or damage which may be caused by viruses.

Hi,

Thank you for your response. This is what I guessed in the first place, but the is no problem with the mesh. I tested the model in other linux machines that I have access and it works fine. I only get this error in my new hpc. I debugged the code in the hpc and I am sure the mesh is read and its information is loaded to the FVCOM correctly but I do not know why tge.f could not handle it. Maybe there is a problem with my intel compiler or required libraries that I installed.
Here is how I installed them:

***OpenMPI
source /share/apps/composer_xe_2015.2.164/bin/compilervars.sh intel64
tar xvzf openmpi-1.6.1.tar.gz

export CC=icc
export CXX=icpc
export FC=ifort
export F90=ifort

./configure --prefix=/home/asafaie/setup/library/openmpi 2>&1 |tee config.out

make all 2>&1 |tee make.out
make install 2>&1 |tee make-install.out
export PATH=/home/asafaie/setup/library/openmpi/bin:$PATH

***NetCDF

tar xvzf netcdf-4.1.3.tar.gz

export CC=icc
export CXX=icpc
export FC=ifort
export F90=ifort

./configure --prefix=/home/asafaie/setup/library/netcdf --disable-netcdf-4

make
make install
make check

***cmake

tar xvzf cmake-2.8.8.tar.gz

export CC=icc
export CXX=icpc
export FC=ifort
export F90=ifort

./configure --prefix=/home/asafaie/setup/library/cmake
make
make install

***METIS
tar xvzf metis-5.0.2.tar.gz

cd /home/asafaie/install/metis-5.0.2
export CC=icc
export CXX=icpc
export FC=ifort
export F90=ifort

make config prefix=/home/asafaie/setup/library/metis
make
make install

[Ricardo Torres]

Am I correct in assuming that you managed to run this setup in a stand alone linux but it fails in your hpc? If that is the case, then maybe the errors are associated with your HPC environment setup. I am afraid that is outside of my area of knowledge. The FVCOM developers do have some instructions on how to install fvcom in a cluster in case they are of any use (http://fvcom.smast.umassd.edu/FVCOM/FVCOMHelp/FVCOM_cluster.html) Regards Ricardo From: asafaie [mailto:[e-mail]] Sent: 14 April 2020 13:33 To: pwcazenave/fvcom-toolbox Cc: Ricardo Torres; Comment Subject: Re: [pwcazenave/fvcom-toolbox] ERROR IN TGE DETERMINING ISONB (#11) Hi Looks like you still have a problem with the mesh or at least information related to the mesh. I am afraid I don’t have any specific advise beyond checking the mesh and setup again. Specially if you have upgraded to the latest fvcom recently. R From: asafaie [mailto:[e-mail]<mailto:[e-mail]>] Sent: 12 April 2020 21:38 To: pwcazenave/fvcom-toolbox Cc: Subscribed Subject: [pwcazenave/fvcom-toolbox] ERROR IN TGE DETERMINING ISONB (#11<#11>) While running FVCOM, I get the following error: FVCOM Fatal Error! ERROR IN TGE DETERMINING ISONB Stopping FVCOM Could you please help me to find the problem? I have previously tested my mesh and input files in another linux machine and the model was working fine. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#11<#11>>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABGHWPZGZWU7OLNGCDLGNFDRMIRAXANCNFSM4MGRTQKQ. …

…

________________________________ This email has been scanned by PML for spam & viruses. If you believe this email should have been stopped by our filters, click herehttps://portal.mailanyone.net/index.html#/outer/reportspam?token=dXNlcj1yaXRvQHBtbC5hYy51azt0cz0xNTg2ODY3NTczO3V1aWQ9NUU5NUFENzREQjdEOEMxMTQ1MDU2MDQzMjA5NkE4NzE7dG9rZW49OGM5ODMxY2UwZjc2Zjk3NThkMTExOTliY2IyZGZlODU3YWU3OTllZDs%3D<https://portal.mailanyone.net/index.html#/outer/reportspam?token=dXNlcj1yaXRvQHBtbC5hYy51azt0cz0xNTg2NzIzODU4O3V1aWQ9NUU5MzdDMTIwRUQxQTgxRTgyNkNBNTc0NTJFQjMwNzc7dG9rZW49MTlkM2I0N2ZjN2Y2YTRlMTNmMWM0MjMwZDVhYzc1Y2QxODJhMjE1MTs%3D> to report it. Please visit our new website at www.pml.ac.uk<http://www.pml.ac.uk> and follow us on Twitter @PlymouthMarine We have updated our Privacy Notice which is available at http://www.pml.ac.uk/System-pages/Privacy_Notice Plymouth Marine Laboratory (PML) is a company limited by guarantee registered in England & Wales, company number 4178503. Registered Charity No. 1091222. Registered Office: Prospect Place, The Hoe, Plymouth PL1 3DH, UK. This message is private and confidential. If you have received this message in error, please notify the sender and remove it from your system. You are reminded that e-mail communications are not secure and may contain viruses; PML accepts no liability for any loss or damage which may be caused by viruses. Hi, Thank you for your response. This is what I guessed in the first place, but the is no problem with the mesh. I tested the model in other linux machines that I have access and it works fine. I only get this error in my new hpc. I debugged the code in the hpc and I am sure the mesh is read and its information is loaded to the FVCOM correctly but I do not know why tge.f could not handle it. Maybe there is a problem with my intel compiler or required libraries that I installed. Here is how I installed them: ***OpenMPI source /share/apps/composer_xe_2015.2.164/bin/compilervars.sh intel64 tar xvzf openmpi-1.6.1.tar.gz export CC=icc export CXX=icpc export FC=ifort export F90=ifort ./configure --prefix=/home/asafaie/setup/library/openmpi 2>&1 |tee config.out make all 2>&1 |tee make.out make install 2>&1 |tee make-install.out export PATH=/home/asafaie/setup/library/openmpi/bin:$PATH ***NetCDF tar xvzf netcdf-4.1.3.tar.gz export CC=icc export CXX=icpc export FC=ifort export F90=ifort ./configure --prefix=/home/asafaie/setup/library/netcdf --disable-netcdf-4 make make install make check ***cmake tar xvzf cmake-2.8.8.tar.gz export CC=icc export CXX=icpc export FC=ifort export F90=ifort ./configure --prefix=/home/asafaie/setup/library/cmake make make install ***METIS tar xvzf metis-5.0.2.tar.gz cd /home/asafaie/install/metis-5.0.2 export CC=icc export CXX=icpc export FC=ifort export F90=ifort make config prefix=/home/asafaie/setup/library/metis make make install — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#11 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABGHWP3YFLVYPBL7WBSERUDRMRJW5ANCNFSM4MGRTQKQ>. Please visit our new website at www.pml.ac.uk and follow us on Twitter @PlymouthMarine We have updated our Privacy Notice which is available at http://www.pml.ac.uk/System-pages/Privacy_Notice Plymouth Marine Laboratory (PML) is a company limited by guarantee registered in England & Wales, company number 4178503. Registered Charity No. 1091222. Registered Office: Prospect Place, The Hoe, Plymouth PL1 3DH, UK. This message is private and confidential. If you have received this message in error, please notify the sender and remove it from your system. You are reminded that e-mail communications are not secure and may contain viruses; PML accepts no liability for any loss or damage which may be caused by viruses.

[asafaie]

Am I correct in assuming that you managed to run this setup in a stand alone linux but it fails in your hpc? If that is the case, then maybe the errors are associated with your HPC environment setup. I am afraid that is outside of my area of knowledge. The FVCOM developers do have some instructions on how to install fvcom in a cluster in case they are of any use (http://fvcom.smast.umassd.edu/FVCOM/FVCOMHelp/FVCOM_cluster.html) Regards Ricardo From: asafaie [mailto:[e-mail]] Sent: 14 April 2020 13:33 To: pwcazenave/fvcom-toolbox Cc: Ricardo Torres; Comment Subject: Re: [pwcazenave/fvcom-toolbox] ERROR IN TGE DETERMINING ISONB (#11) Hi Looks like you still have a problem with the mesh or at least information related to the mesh. I am afraid I don’t have any specific advise beyond checking the mesh and setup again. Specially if you have upgraded to the latest fvcom recently. R From: asafaie [mailto:[e-mail]:[e-mail]] Sent: 12 April 2020 21:38 To: pwcazenave/fvcom-toolbox Cc: Subscribed Subject: [pwcazenave/fvcom-toolbox] ERROR IN TGE DETERMINING ISONB (#11<#11>) While running FVCOM, I get the following error: FVCOM Fatal Error! ERROR IN TGE DETERMINING ISONB Stopping FVCOM Could you please help me to find the problem? I have previously tested my mesh and input files in another linux machine and the model was working fine. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#11<#11>>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABGHWPZGZWU7OLNGCDLGNFDRMIRAXANCNFSM4MGRTQKQ. …
…
________________________________ This email has been scanned by PML for spam & viruses. If you believe this email should have been stopped by our filters, click herehttps://portal.mailanyone.net/index.html#/outer/reportspam?token=dXNlcj1yaXRvQHBtbC5hYy51azt0cz0xNTg2ODY3NTczO3V1aWQ9NUU5NUFENzREQjdEOEMxMTQ1MDU2MDQzMjA5NkE4NzE7dG9rZW49OGM5ODMxY2UwZjc2Zjk3NThkMTExOTliY2IyZGZlODU3YWU3OTllZDs%3Dhttps://portal.mailanyone.net/index.html#/outer/reportspam?token=dXNlcj1yaXRvQHBtbC5hYy51azt0cz0xNTg2NzIzODU4O3V1aWQ9NUU5MzdDMTIwRUQxQTgxRTgyNkNBNTc0NTJFQjMwNzc7dG9rZW49MTlkM2I0N2ZjN2Y2YTRlMTNmMWM0MjMwZDVhYzc1Y2QxODJhMjE1MTs%3D to report it. Please visit our new website at www.pml.ac.uk<http://www.pml.ac.uk> and follow us on Twitter @PlymouthMarine We have updated our Privacy Notice which is available at http://www.pml.ac.uk/System-pages/Privacy_Notice Plymouth Marine Laboratory (PML) is a company limited by guarantee registered in England & Wales, company number 4178503. Registered Charity No. 1091222. Registered Office: Prospect Place, The Hoe, Plymouth PL1 3DH, UK. This message is private and confidential. If you have received this message in error, please notify the sender and remove it from your system. You are reminded that e-mail communications are not secure and may contain viruses; PML accepts no liability for any loss or damage which may be caused by viruses. Hi, Thank you for your response. This is what I guessed in the first place, but the is no problem with the mesh. I tested the model in other linux machines that I have access and it works fine. I only get this error in my new hpc. I debugged the code in the hpc and I am sure the mesh is read and its information is loaded to the FVCOM correctly but I do not know why tge.f could not handle it. Maybe there is a problem with my intel compiler or required libraries that I installed. Here is how I installed them: ***OpenMPI source /share/apps/composer_xe_2015.2.164/bin/compilervars.sh intel64 tar xvzf openmpi-1.6.1.tar.gz export CC=icc export CXX=icpc export FC=ifort export F90=ifort ./configure --prefix=/home/asafaie/setup/library/openmpi 2>&1 |tee config.out make all 2>&1 |tee make.out make install 2>&1 |tee make-install.out export PATH=/home/asafaie/setup/library/openmpi/bin:$PATH ***NetCDF tar xvzf netcdf-4.1.3.tar.gz export CC=icc export CXX=icpc export FC=ifort export F90=ifort ./configure --prefix=/home/asafaie/setup/library/netcdf --disable-netcdf-4 make make install make check ***cmake tar xvzf cmake-2.8.8.tar.gz export CC=icc export CXX=icpc export FC=ifort export F90=ifort ./configure --prefix=/home/asafaie/setup/library/cmake make make install ***METIS tar xvzf metis-5.0.2.tar.gz cd /home/asafaie/install/metis-5.0.2 export CC=icc export CXX=icpc export FC=ifort export F90=ifort make config prefix=/home/asafaie/setup/library/metis make make install — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#11 (comment)>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABGHWP3YFLVYPBL7WBSERUDRMRJW5ANCNFSM4MGRTQKQ. Please visit our new website at www.pml.ac.uk and follow us on Twitter @PlymouthMarine We have updated our Privacy Notice which is available at http://www.pml.ac.uk/System-pages/Privacy_Notice Plymouth Marine Laboratory (PML) is a company limited by guarantee registered in England & Wales, company number 4178503. Registered Charity No. 1091222. Registered Office: Prospect Place, The Hoe, Plymouth PL1 3DH, UK. This message is private and confidential. If you have received this message in error, please notify the sender and remove it from your system. You are reminded that e-mail communications are not secure and may contain viruses; PML accepts no liability for any loss or damage which may be caused by viruses.

I was previously successful to compile and run FVCOM with this setup in both stand alone linux machines and hpcs, but it fails this time and it's been a month that I am not able to solve this issue.
Thank you Ricardo.

Ammar