Issue Compiling MAKEIC.so with WRAPIT

[Will Smith]

Hi all,

I am currently using the IPT tool to to regrid MERRA2 data. The original MERRA2 data are from NCAR machine. Following the instructions, I attempted to use WRAPIT to compile MAKEIC.so using NCL/6.6.2. However, I keep running into the following error:

WRAPIT Version: 120209
*** buffer overflow detected ***: terminated
Abort
FATAL ERROR: wrapit77 failed

I then gave it a go with gfortran, but that also didn’t work out—the log file with the error details is attached.

warning:Could not find Init() in external file ./MAKEIC.so, file not loaded

Do you think this might be an issue with the original IPT code? I’m running everything on a non-NCAR machine, so I wonder if that could be playing a part.

Any suggestions would be hugely appreciated. Thanks so much in advance!

 

[hplin]

Hello Will Smith, thanks for writing. I believe the IPT tools are managed by the MUSICA team so I will move this to the CAM-chem forum.

I would suggest trying to WRAPIT an example script (maybe from here NCL: WRAPIT) to see if WRAPIT is running correctly on your system, which hopefully will help narrow down the problem to IPT or the NCL installation.

 

[Will Smith]

Hello Will Smith, thanks for writing. I believe the IPT tools are managed by the MUSICA team so I will move this to the CAM-chem forum.

I would suggest trying to WRAPIT an example script (maybe from here NCL: WRAPIT) to see if WRAPIT is running correctly on your system, which hopefully will help narrow down the problem to IPT or the NCL installation.

Thanks for the tip! I will give it a go.

 

[Will Smith]

Just a quick update, when I followed the instructions to test WRAPIT, it ran without any errors.

Below is the result I got when I used the command WRAPIT -d MAKEIC.stub MAKEIC.f90:

WRAPIT Version: 120209
OPERATING SYSTEM: Linux
nbits = 64
FORTRAN COMPILER (f90c): gfortran
FORTRAN COMPILER OPTIONS (fopts): -m64 -fPIC -v -c -fno-second-underscore
*** buffer overflow detected ***: terminated
Abort
FATAL ERROR: wrapit77 failed

Please let me know if you have any suggestions on how to resolve this issue

 

[hplin]

Thanks for the update. Is the same error occurring for all the MAKEICs under IPT?

I wonder if the system limits (ulimit) may also be causing this. Could you try building this on a compute node on the cluster or increasing the ulimit stack size limit (ulimit -s <limit>) to see if it'll help?

 

[Will Smith]

Thanks for the update. Is the same error occurring for all the MAKEICs under IPT?

I wonder if the system limits (ulimit) may also be causing this. Could you try building this on a compute node on the cluster or increasing the ulimit stack size limit (ulimit -s <limit>) to see if it'll help?

Hi Lin,

I tried running WRAPIT on the compute node, and this time it successfully compiled the MAKEIC.so file. However, when I ran the final script, I got the following error:
Copyright (C) 1995-2019 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.6.2
The use of this software is governed by a Licence Agreement.
See NCAR Command Language (NCL) for more details.
warning:Could not find Init() in external file ./MAKEIC.so, file not loaded
warning:error at line 12 in file makeIC_se_002.ncl

I've attached the log file for more details. I also tried adding the following to the end of the MAKEIC.f90 file to solve the issue:

subroutine Init()
call makeic()
end subroutine Init

Then I recompiled, MAKEIC.so was there, but I still got the same error when running the final script. Is there anything else I could try?

Many thanks

 

[Will Smith]

Hi all,

While the MAKEIC.so file is generated, I have encountered some errors during the process.
The first error appears as follows:

A syntax error occurred while parsing: realC
(logfile slurm-9355051.out)

Then, when attempting to run the final script using the generated MAKEIC.so, I received the following warning:

warning: Could not find Init() in external file ./MAKEIC.so, file not loaded
warning: error at line 12 in file makeIC_se_002.ncl
(logfile LogNCL.2018010100000)

The corresponding log file contains more details about the errors. So whether there might be an issue with the MAKEIC.stub or MAKEIC.f90 scripts provided in the IPT tool that could be causing this problem?

Any guidance or suggestions would be greatly appreciated.

 

[rrbuchholz]

Hi Will,

Apparently sometimes there are issues with using different versions of NCL. If you were on the UCAR HPC we would recommend to point to ncl version 6.6.2:

replace WRAPIT -d MAKEIC.stub MAKEIC.f90 with

/glade/u/apps/opt/ncl/6.6.2/bin/WRAPIT MAKEIC.stub MAKEIC.f90

It looks like perhaps you are already using NCL 6.6.2?
What happens if you use and alternate version of NCL?

Best,
Rebecca

 

[Will Smith]

Hi Will,

Apparently sometimes there are issues with using different versions of NCL. If you were on the UCAR HPC we would recommend to point to ncl version 6.6.2:



It looks like perhaps you are already using NCL 6.6.2?
What happens if you use and alternate version of NCL?

Best,
Rebecca

Hi Rebecca,

Thanks for your message!

I don't have access to the NCAR HPC system, but I am using NCL version 6.6.2 on my current platform (Archer2 the UK HPC). Do I need to load any additional modules for that? like gcc

Many thanks,
Will

 

[rrbuchholz]

Hi Will,

I'm not really sure, I have not really used IPT (Shawn is the current expert in that, who is responding on your other question). We just uploaded a new version of IPT, so I wonder if that might fix the problem.

MUSICA-Tools/IPT/Meterological_Reanalysis_Data at main · NCAR/MUSICA-Tools

Tools to be used with atmospheric chemistry modeling - NCAR/MUSICA-Tools

github.com

Best,
Rebecca

 

[Will Smith]

Hi Will,

I'm not really sure, I have not really used IPT (Shawn is the current expert in that, who is responding on your other question). We just uploaded a new version of IPT, so I wonder if that might fix the problem.

MUSICA-Tools/IPT/Meterological_Reanalysis_Data at main · NCAR/MUSICA-Tools

Tools to be used with atmospheric chemistry modeling - NCAR/MUSICA-Tools

github.com

Best,
Rebecca

Hi Rebecca,

Thank you very much for the update and the link! I’ll check out the new version of IPT — hopefully that resolves the issue. Appreciate your help.

Best,
Will