# "NetCDF: Malformed URL" issue encountered during the MCIP process
**URL:** https://forum.cmascenter.org/t/netcdf-malformed-url-issue-encountered-during-the-mcip-process/5565
**Category:** MCIP
**Created:** [February 3, 2025, 2:01pm UTC](https://forum.cmascenter.org/t/netcdf-malformed-url-issue-encountered-during-the-mcip-process/5565 "2025-02-03T14:01:55Z")
**Posts on this page:** 8
**Page:** 1
### Author:  [@wenxing](https://forum.cmascenter.org/u/wenxing)
#### Post date: [February 3, 2025, 2:01pm UTC](https://forum.cmascenter.org/t/netcdf-malformed-url-issue-encountered-during-the-mcip-process/5565/1 "2025-02-03T14:01:55Z")
Hello everone. I am a student studying MCIP and am currently encountering some issues while running it. Could you please provide some guidance? The problem is shown in the screenshot below:
- I have tried various combinations of WRF and MCIP versions (including all combinations of WRF v4.2 to v4.5 with CMAQ v5.3 and v5.4), but all of them report the same error.
- When I run `nc-config --all`and `nf-config --all` , the output is as follows:
- I have uploaded the output file generated by running `ncdump -h [file] >&log.txt&`.
[log.txt](https://forum.cmascenter.org/uploads/short-url/8eg6flOdLDbXpKhSucc7Un1hxl1.txt) (55.3 KB)
- When I run `ls -l`, showed:
`-rw-r--r-- 1 a67934wf fatpou01 226398400 Feb 2 17:43 /net/scratch2/a67934wf/WRF_out_36_new/wrfout_d01_2019-01-01_00:00:00`
- I have uploaded my `namelist.input.txt` file and `run_mcip.csh` file.
[namelist.input.txt](https://forum.cmascenter.org/uploads/short-url/rccnXPDrhpg21l6orfAOBg9F3Qy.txt) (10.7 KB)
[run\_mcip.csh](https://forum.cmascenter.org/uploads/short-url/soNO38wxrOxsYELbYU7oUGIUqZ5.csh) (18.8 KB)
- My environment variables are set as follows:
- My I/O API version is 3.2.
- My compiler is gcc@8.2.0.
I hope to receive everyone’s guidance and help. Thank you all!!
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### Author:  [@tlspero](https://forum.cmascenter.org/u/tlspero)
#### Post date: [February 4, 2025, 4:24pm UTC](https://forum.cmascenter.org/t/netcdf-malformed-url-issue-encountered-during-the-mcip-process/5565/2 "2025-02-04T16:24:13Z")
Hi @wenxing!
Thank you for opening a new thread.
I have one suggestion for you to try before I dive in. Please consider renaming your WRF output file to “wrfout” and try running again with that file name in the script. This will eliminate whether there is a character in the long file name that is causing the error.
If that test also fails, then we will have additional information to guide the next steps.
–Tanya
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### Author:  [@wenxing](https://forum.cmascenter.org/u/wenxing)
#### Post date: [February 4, 2025, 4:47pm UTC](https://forum.cmascenter.org/t/netcdf-malformed-url-issue-encountered-during-the-mcip-process/5565/3 "2025-02-04T16:47:58Z")
Hi Tanya,
Thank you for your quick response.
I have followed your suggestion and renamed the WRF output file to “wrfout” but the error still persists. Additionally, I tried linking the file to the current working directory, but the same issue remains.
I look forward to your reply. Thanks again for your help!
— Wenxing
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### Author:  [@tlspero](https://forum.cmascenter.org/u/tlspero)
#### Post date: [February 4, 2025, 5:25pm UTC](https://forum.cmascenter.org/t/netcdf-malformed-url-issue-encountered-during-the-mcip-process/5565/4 "2025-02-04T17:25:07Z")
@wenxing –
Thank you for making the quick test and posting the results here. That was helpful.
I looked back at your initial post–and thank you for all of the great background on this issue. I focused on this excerpt:
If I understand correctly, “a67934wf” is supposed to be a directory in the path of the WRF output file. However, the permissions do not have “execute” among them, so you cannot change directories to explore the contents of “a67934wf” or any of its subdirectories.
If this is the case, please go to /net/scratch2 and type the command:
chmod 755 a67934wf
This command adds “execute” privileges to the directory “a67934aw”, which allows you to change directories. After you execute the command and type “ls -l”, then you should see the following pattern ahead of the directory name:
-rwxr-xr-x
_Edited to add: If you do not own the directory “a67934wf”, then the directory owner will need to modify the permissions to add “execute” privileges so that the contents of the directory can be explored._
Hope this helps.
Tanya
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### Author:  [@cgnolte](https://forum.cmascenter.org/u/cgnolte)
#### Post date: [February 4, 2025, 6:00pm UTC](https://forum.cmascenter.org/t/netcdf-malformed-url-issue-encountered-during-the-mcip-process/5565/5 "2025-02-04T18:00:34Z")
It would not be possible to ls -l the file, or ncdump its header, if there is no execute permission on the directory, so I think that is not the problem.
You might try copying the file from /net/scratch2 onto the same disk from which you are running mcip. Maybe the way you are submitting the job, the mcip executable does not have access to /net/scratch2.
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### Author:  [@tlspero](https://forum.cmascenter.org/u/tlspero)
#### Post date: [February 4, 2025, 6:14pm UTC](https://forum.cmascenter.org/t/netcdf-malformed-url-issue-encountered-during-the-mcip-process/5565/6 "2025-02-04T18:14:27Z")
Yes, @cgnolte is correct. I misread the “ls -l” excerpt to be two separate lines. Looking at it with that lens, I think “a67934wf” is actually the user ID for @wenxing, so please disregard my last post.
I think there is something wrong with the file permissions, though, as @cgnolte also suggested.
–Tanya
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### Author:  [@wenxing](https://forum.cmascenter.org/u/wenxing)
#### Post date: [February 27, 2025, 6:42pm UTC](https://forum.cmascenter.org/t/netcdf-malformed-url-issue-encountered-during-the-mcip-process/5565/7 "2025-02-27T18:42:16Z")
Hi @cgnolte @tlspero , apologies for the late response. I’ve been actively working to resolve the issue recently and, with the help of our teacher managing the servers, have managed to solve the error. Here are the steps we took that might help others facing similar issues:
1. We recompiled the dependent environment and CMAQv5.4, specifically focusing on ensuring consistent compiler versions across WRF, libraries, and CMAQ.
2. We configured netcdf with specific settings and recompiled ioapi with this version of netcdf.
3.However, we compiled MCIP and CMAQ using a netcdf version with has\_dap=“yes” and has\_dap4=“yes.” Otherwise, they would throw the error “Attempt to use feature that was not turned on when netCDF was built.”
Although I’m still not sure which step exactly resolved the critical issue, everything is running smoothly now. Thanks again for your help and guidance !
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### Author:  [@tlspero](https://forum.cmascenter.org/u/tlspero)
#### Post date: [February 27, 2025, 9:26pm UTC](https://forum.cmascenter.org/t/netcdf-malformed-url-issue-encountered-during-the-mcip-process/5565/8 "2025-02-27T21:26:13Z")
@wenxing –
I’m glad to hear that it is working now for you. Thank you for reporting back and documenting the process you used to overcome the error!
–Tanya