Compiling source

[AmirrezaHBSH]

Hello, I downloaded the FDS source to my cluster using the command: git clone. However, I encountered an issue while compiling the code. The error indicates the presence of ^M characters in the code, which need to be removed for successful compilation. I'm seeking advice on alternative or improved methods for downloading the code to the cluster to prevent encountering this error in the future.

[mcgratta]

Our default and preferred text file format is unix/linux. Can you tell us which file is causing the issue?

[AmirrezaHBSH]

I am not sure which file is causing the issue, since I am a new user. In the Fire models when I want to compile fds file, I face with this issue. I am using PuTTY.

[gforney]

by any chance did you clone the fds repo on a Windows PC then copy the files to a Linux or Mac ? if so you need to use the git clone command on the computer where the files will reside

[AmirrezaHBSH]

No, I just downloaded the fds repo directly to the cluster by using PuTTY

[mcgratta]

I see that imkl.f90 looks MacOS-y. I'll look for others.

[mcgratta]

My vi editor tells me this

"imkl.f90" [noeol] 197L, 9271C

But this has never caused us any trouble.

[mcgratta]

I changed one file but I doubt that this is the cause of your issue. You could update the repo and try again.

[AmirrezaHBSH]

How can I download just that edited file in my cluster?

[TristanHehnen]

On the Linux machine, navigate to your git repo and execute git pull.

[mcgratta]

I have never used PuTTy to clone a git repository. How did you do it?

[AmirrezaHBSH]

I used this command: git clone git@github.com:firemodels/fds.git

[TristanHehnen]

There may be a misunderstanding here.
Putty is used to enable an ssh connection from Windows machines to Linux. One would end up with a regular Linux terminal on the remote machine.

https://hub.wpi.edu/article/785/connect-to-linux-cluster-on-windows-using-putty

Thus, the git clone should be a regular terminal interaction and nothing specific to putty itself.

[mcgratta]

OK, thanks. So assuming that the fds repository has been cloned directly onto your linux-based cluster. How exactly are you trying to compile the code?

[AmirrezaHBSH]

I am using ompi-gnu-linux, and make fds.sh. In this step I can see an error of ^M. then I am removing this character then compiling.

[mcgratta]

Do you know what file has the ^M character?

[AmirrezaHBSH]

:ompi_gnu_linux> ./make_fds.sh
-bash: ./make_fds.sh: /bin/bash^M: bad interpreter: No such file or directory

This is the error I have when compiling fds all files. Could you please tell me how I can search for the exact file to see which file is causing this issue?

[mcgratta]

This appears to be a problem with the file make_fds.sh. Open this file with the vi editor and you should see this

#!/bin/bash
dir=`pwd`
target=${dir##*/}

echo Building $target
make -j4 VPATH="../../Source" -f ../makefile $target
~
~
"make_fds.sh" 6L, 116C                                     

Make sure that is does not say DOS at the bottom. Then at the command prompt, type the command ls -l

ls -l
total 8
-rwxr-xr-x. 1 mcgratta div733 116 Nov 29  2022 make_fds.sh

Do you see the same arrangement of r's and x's indicating that the file is an executable script? If not

chmod +x make_fds.sh

[AmirrezaHBSH]

Thank you for your reply, however, vi editor does not show anything inside the make_fds.sh

[AmirrezaHBSH]

Yes I got it there is DOS at the bottom. How should I procced?

[mcgratta]

Quick solution would be to change the file make_fds.sh to unix format. I do this by opening the file with vi and then type

set ff=unix

Then wq to exit. Longer term, you should figure out why your cloning of the repository changed the line endings.

[AmirrezaHBSH]

Where should I type this set ff=unix? at the beginning of the vi editor?

[mcgratta]

:set ff=unix

This is a command issued by the editor. The colon gives you a prompt

[AmirrezaHBSH]

I appreciate. I did that got this error:

Building ompi_gnu_linux
/bin/bash: ../Scripts/osx_clt.sh: /bin/bash^M: bad interpreter: No such file or directory
mpifort -c -m64 -O2 -std=f2018 -frecursive -ffpe-summary=none -fall-intrinsics -cpp -DGITHASH_PP="FDS-6.9.0-13-gd1b1af3-master" -DGITDATE_PP=""Wed Mar 27 09:36:17 2024 -0400"" -DBUILDDATE_PP=""Mar 27, 2024 10:05:34"" ../../Source/prec.f90
mpifort -c -m64 -O2 -std=f2018 -frecursive -ffpe-summary=none -fall-intrinsics -cpp -DGITHASH_PP="FDS-6.9.0-13-gd1b1af3-master" -DGITDATE_PP=""Wed Mar 27 09:36:17 2024 -0400"" -DBUILDDATE_PP=""Mar 27, 2024 10:05:34"" ../../Source/imkl.f90
/bin/bash: mpifort: command not found
make: *** [../makefile:121: prec.o] Error 127
make: *** Waiting for unfinished jobs....
/bin/bash: mpifort: command not found
make: *** [../makefile:121: imkl.o] Error 127

[marcosvanella]

You have to have openmpi loaded in your environment to have access to mpifort. Ask your cluster IT person.
Also do the same change to unix on the script in Build/Scripts/osx_clt.sh. Somehow you got these ^M DOS end of line characters when cloning the repo.

[mcgratta]

You need IT support for the particular computer you are using. We cannot help you solve issues related to the installation of software on your computer.