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cesm1_2_2_CAMChem Running Issue - NetCDF: Invalid dimension ID or name

J

jedwards

CSEG and Liaisons
Staff member
It looks like the last file opened by cam is corrupted or in a format not recognized by your netcdf.   Look in the atm.log to determine what that file is, then use ncdump -k to determine the format of that file, you might try removing the file so that it will be downloaded again, often this will solve the problem
 
V

vineetm@cdac_in

Member
Thanks for the fast reply jedwards.I tried what you told, perhaps netcdf is not configured correctly I suppose.I also deleted the file so that it is downloaded again and verified. Still having the same issue.I have attached a screenshot for the info along with the generated logs. Please let me know if the file is itself in wrong format or my netcdf installation is faulty. I am sorry I am taking this issue to a totally different discussion. Please also let me know if commenting on this thread is ok.Also, let me know if I should go with a different case for testing the installation.Also I checked the other files downloaded in my DATA directory and found out that many files are showing the same message. I insist you to also check the Additional Info.txt file in the atttachments.Should any flag be enabled in netcdf to read some specific files? Thanks,Vineet
 
V

vineetm@cdac_in

Member
Thanks for the fast reply jedwards.I tried what you told, perhaps netcdf is not configured correctly I suppose.I also deleted the file so that it is downloaded again and verified. Still having the same issue.I have attached a screenshot for the info along with the generated logs. Please let me know if the file is itself in wrong format or my netcdf installation is faulty. I am sorry I am taking this issue to a totally different discussion. Please also let me know if commenting on this thread is ok.Also, let me know if I should go with a different case for testing the installation.Also I checked the other files downloaded in my DATA directory and found out that many files are showing the same message. I insist you to also check the Additional Info.txt file in the atttachments.Should any flag be enabled in netcdf to read some specific files? Thanks,Vineet
 
V

vineetm@cdac_in

Member
Thanks for the fast reply jedwards.I tried what you told, perhaps netcdf is not configured correctly I suppose.I also deleted the file so that it is downloaded again and verified. Still having the same issue.I have attached a screenshot for the info along with the generated logs. Please let me know if the file is itself in wrong format or my netcdf installation is faulty. I am sorry I am taking this issue to a totally different discussion. Please also let me know if commenting on this thread is ok.Also, let me know if I should go with a different case for testing the installation.Also I checked the other files downloaded in my DATA directory and found out that many files are showing the same message. I insist you to also check the Additional Info.txt file in the atttachments.Should any flag be enabled in netcdf to read some specific files? Thanks,Vineet
 
V

vineetm@cdac_in

Member
Thanks for the fast reply jedwards.I tried what you told, perhaps netcdf is not configured correctly I suppose.I also deleted the file so that it is downloaded again and verified. Still having the same issue.I have attached a screenshot for the info along with the generated logs. Please let me know if the file is itself in wrong format or my netcdf installation is faulty. I am sorry I am taking this issue to a totally different discussion. Please also let me know if commenting on this thread is ok.Also, let me know if I should go with a different case for testing the installation.Also I checked the other files downloaded in my DATA directory and found out that many files are showing the same message. I insist you to also check the Additional Info.txt file in the atttachments.Should any flag be enabled in netcdf to read some specific files? Thanks,Vineet
 
V

vineetm@cdac_in

Member
Thanks for the fast reply jedwards.I tried what you told, perhaps netcdf is not configured correctly I suppose.I also deleted the file so that it is downloaded again and verified. Still having the same issue.I have attached a screenshot for the info along with the generated logs. Please let me know if the file is itself in wrong format or my netcdf installation is faulty. I am sorry I am taking this issue to a totally different discussion. Please also let me know if commenting on this thread is ok.Also, let me know if I should go with a different case for testing the installation.Also I checked the other files downloaded in my DATA directory and found out that many files are showing the same message. I insist you to also check the Additional Info.txt file in the atttachments.Should any flag be enabled in netcdf to read some specific files? Thanks,Vineet
 
J

jedwards

CSEG and Liaisons
Staff member
The error is definitly that it cannot open that file, but I don't see the reason.  Check the md5sum of the file, it should be:08f4ca5459849edaceb992738df523cb 
 
J

jedwards

CSEG and Liaisons
Staff member
The error is definitly that it cannot open that file, but I don't see the reason.  Check the md5sum of the file, it should be:08f4ca5459849edaceb992738df523cb 
 
J

jedwards

CSEG and Liaisons
Staff member
The error is definitly that it cannot open that file, but I don't see the reason.  Check the md5sum of the file, it should be:08f4ca5459849edaceb992738df523cb 
 
J

jedwards

CSEG and Liaisons
Staff member
The error is definitly that it cannot open that file, but I don't see the reason.  Check the md5sum of the file, it should be:08f4ca5459849edaceb992738df523cb 
 
J

jedwards

CSEG and Liaisons
Staff member
The error is definitly that it cannot open that file, but I don't see the reason.  Check the md5sum of the file, it should be:08f4ca5459849edaceb992738df523cb 
 
V

vineetm@cdac_in

Member
Thanks jedwards, the file was indeed not correctly downloaded.Well now everything is going all well.Can you please let me know approximately how much average time will the below model take to complete../create_newcase --case /scratch/vineetm/CESM_NEW/CASE_DEBUG --compset B1850 --res f19_g17 --mach ported_machBecause now its been aroung 5 and a half days the model is still running on 6 nodes 8 processes each (with the default settings.)Thanks
 
V

vineetm@cdac_in

Member
Thanks jedwards, the file was indeed not correctly downloaded.Well now everything is going all well.Can you please let me know approximately how much average time will the below model take to complete../create_newcase --case /scratch/vineetm/CESM_NEW/CASE_DEBUG --compset B1850 --res f19_g17 --mach ported_machBecause now its been aroung 5 and a half days the model is still running on 6 nodes 8 processes each (with the default settings.)Thanks
 
V

vineetm@cdac_in

Member
Thanks jedwards, the file was indeed not correctly downloaded.Well now everything is going all well.Can you please let me know approximately how much average time will the below model take to complete../create_newcase --case /scratch/vineetm/CESM_NEW/CASE_DEBUG --compset B1850 --res f19_g17 --mach ported_machBecause now its been aroung 5 and a half days the model is still running on 6 nodes 8 processes each (with the default settings.)Thanks
 
V

vineetm@cdac_in

Member
Thanks jedwards, the file was indeed not correctly downloaded.Well now everything is going all well.Can you please let me know approximately how much average time will the below model take to complete../create_newcase --case /scratch/vineetm/CESM_NEW/CASE_DEBUG --compset B1850 --res f19_g17 --mach ported_machBecause now its been aroung 5 and a half days the model is still running on 6 nodes 8 processes each (with the default settings.)Thanks
 
V

vineetm@cdac_in

Member
Thanks jedwards, the file was indeed not correctly downloaded.Well now everything is going all well.Can you please let me know approximately how much average time will the below model take to complete../create_newcase --case /scratch/vineetm/CESM_NEW/CASE_DEBUG --compset B1850 --res f19_g17 --mach ported_machBecause now its been aroung 5 and a half days the model is still running on 6 nodes 8 processes each (with the default settings.)Thanks
 
V

vineetm@cdac_in

Member
Hi Jedwards,I have managed to get the cesm1_2_2_CAMChem up and running.The case that is created is using the command below:
create_newcase -case /scratch/cc/vfaculty/rsoniya.vfaculty/CASES/CASE1 -res T31_g37 -compset F1850CNCHM -mach The model runs fine and stops in two cases: 1) When using PIO_TYPENAME = netcdf : Here some pio error occurs.  (Refer log : CASE1.o762972 and CASE1.o762972_log)Netcdf seems to be build correctly. Below is the log:[rsoniya.vfaculty@login02 CASE1]$ nc-config --all This netCDF 4.3.3.1 has been built with the following features:   --cc        -> mpicc  --cflags    ->  -I/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/include -I/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/include  --libs      -> -L/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/lib -lnetcdf   --has-c++   -> no  --cxx       ->  --has-c++4  -> no  --cxx4      ->   --fc        -> mpifort  --fflags    -> -I/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/include  --flibs     -> -L/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/lib -lnetcdff -L/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/lib -lnetcdf -lnetcdf  --has-f90   -> no   --has-dap   -> yes  --has-nc2   -> yes  --has-nc4   -> yes  --has-hdf5  -> yes  --has-hdf4  -> no  --has-pnetcdf-> yes   --prefix    -> /scratch/cc/vfaculty/rsoniya.vfaculty/install/deps  --includedir-> /scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/include  --version   -> netCDF 4.3.3.1 2) When using PIO_TYPENAME = pnetcdf. (Refer log : CASE1.o763026 and CASE1.o763026_log - these are with debug) Sorry, for stretching this thread too much. But it would be helpful.Thanks,Vineet More
 
V

vineetm@cdac_in

Member
Hi Jedwards,I have managed to get the cesm1_2_2_CAMChem up and running.The case that is created is using the command below:
create_newcase -case /scratch/cc/vfaculty/rsoniya.vfaculty/CASES/CASE1 -res T31_g37 -compset F1850CNCHM -mach The model runs fine and stops in two cases: 1) When using PIO_TYPENAME = netcdf : Here some pio error occurs.  (Refer log : CASE1.o762972 and CASE1.o762972_log)Netcdf seems to be build correctly. Below is the log:[rsoniya.vfaculty@login02 CASE1]$ nc-config --all This netCDF 4.3.3.1 has been built with the following features:   --cc        -> mpicc  --cflags    ->  -I/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/include -I/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/include  --libs      -> -L/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/lib -lnetcdf   --has-c++   -> no  --cxx       ->  --has-c++4  -> no  --cxx4      ->   --fc        -> mpifort  --fflags    -> -I/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/include  --flibs     -> -L/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/lib -lnetcdff -L/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/lib -lnetcdf -lnetcdf  --has-f90   -> no   --has-dap   -> yes  --has-nc2   -> yes  --has-nc4   -> yes  --has-hdf5  -> yes  --has-hdf4  -> no  --has-pnetcdf-> yes   --prefix    -> /scratch/cc/vfaculty/rsoniya.vfaculty/install/deps  --includedir-> /scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/include  --version   -> netCDF 4.3.3.1 2) When using PIO_TYPENAME = pnetcdf. (Refer log : CASE1.o763026 and CASE1.o763026_log - these are with debug) Sorry, for stretching this thread too much. But it would be helpful.Thanks,Vineet More
 
V

vineetm@cdac_in

Member
Hi Jedwards,I have managed to get the cesm1_2_2_CAMChem up and running.The case that is created is using the command below:
create_newcase -case /scratch/cc/vfaculty/rsoniya.vfaculty/CASES/CASE1 -res T31_g37 -compset F1850CNCHM -mach The model runs fine and stops in two cases: 1) When using PIO_TYPENAME = netcdf : Here some pio error occurs.  (Refer log : CASE1.o762972 and CASE1.o762972_log)Netcdf seems to be build correctly. Below is the log:[rsoniya.vfaculty@login02 CASE1]$ nc-config --all This netCDF 4.3.3.1 has been built with the following features:   --cc        -> mpicc  --cflags    ->  -I/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/include -I/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/include  --libs      -> -L/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/lib -lnetcdf   --has-c++   -> no  --cxx       ->  --has-c++4  -> no  --cxx4      ->   --fc        -> mpifort  --fflags    -> -I/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/include  --flibs     -> -L/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/lib -lnetcdff -L/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/lib -lnetcdf -lnetcdf  --has-f90   -> no   --has-dap   -> yes  --has-nc2   -> yes  --has-nc4   -> yes  --has-hdf5  -> yes  --has-hdf4  -> no  --has-pnetcdf-> yes   --prefix    -> /scratch/cc/vfaculty/rsoniya.vfaculty/install/deps  --includedir-> /scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/include  --version   -> netCDF 4.3.3.1 2) When using PIO_TYPENAME = pnetcdf. (Refer log : CASE1.o763026 and CASE1.o763026_log - these are with debug) Sorry, for stretching this thread too much. But it would be helpful.Thanks,Vineet More
 
V

vineetm@cdac_in

Member
Hi Jedwards,I have managed to get the cesm1_2_2_CAMChem up and running.The case that is created is using the command below:
create_newcase -case /scratch/cc/vfaculty/rsoniya.vfaculty/CASES/CASE1 -res T31_g37 -compset F1850CNCHM -mach The model runs fine and stops in two cases: 1) When using PIO_TYPENAME = netcdf : Here some pio error occurs.  (Refer log : CASE1.o762972 and CASE1.o762972_log)Netcdf seems to be build correctly. Below is the log:[rsoniya.vfaculty@login02 CASE1]$ nc-config --all This netCDF 4.3.3.1 has been built with the following features:   --cc        -> mpicc  --cflags    ->  -I/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/include -I/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/include  --libs      -> -L/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/lib -lnetcdf   --has-c++   -> no  --cxx       ->  --has-c++4  -> no  --cxx4      ->   --fc        -> mpifort  --fflags    -> -I/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/include  --flibs     -> -L/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/lib -lnetcdff -L/scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/lib -lnetcdf -lnetcdf  --has-f90   -> no   --has-dap   -> yes  --has-nc2   -> yes  --has-nc4   -> yes  --has-hdf5  -> yes  --has-hdf4  -> no  --has-pnetcdf-> yes   --prefix    -> /scratch/cc/vfaculty/rsoniya.vfaculty/install/deps  --includedir-> /scratch/cc/vfaculty/rsoniya.vfaculty/install/deps/include  --version   -> netCDF 4.3.3.1 2) When using PIO_TYPENAME = pnetcdf. (Refer log : CASE1.o763026 and CASE1.o763026_log - these are with debug) Sorry, for stretching this thread too much. But it would be helpful.Thanks,Vineet More
 
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