Hi Molly,
Apologies for the “-framework accelerate” option - this is for Mac computers to enable the fast maths libraries, but won’t work on Linux. I’ve switched the default so that this isn’t present. You can edit mkgulp and edit the line with this option to remove it (or uncomment the line just above without it and comment the line with it).
The “-fallow-argument-mismatch” is covered in the README file. This means you have an old version of gfortran (before v10) where this option didn’t exist. You can fix by either updating your compiler or remove/comment as above.
Regards,
Julian
Hi Julian,
I hope you are doing well. I’m trying to install Gulp but keep facing these issues:
I am getting almost the same error as Molly got when performing the command ./mkgulp
[cd …/…/Utils/pGFNFF/Src/; make FC=‘gfortran -fallow-argument-mismatch ’ FCFLAGS=’-O3 -ffpe-summary=invalid,zero,overflow -I… ’
make[1]: Entering directory ‘/mnt/c/Users/Samaneh/gulp-6.1/Utils/pGFNFF/Src’
gfortran -fallow-argument-mismatch -O3 -ffpe-summary=invalid,zero,overflow -I… -c m_pgfnff_types.F90
gfortran: error: unrecognized command line option ‘-fallow-argument-mismatch’; did you mean ‘-Wno-argument-mismatch’?
make[1]: *** [Makefile:111: m_pgfnff_types.o] Error 1
make[1]: Leaving directory ‘/mnt/c/Users/Samaneh/gulp-6.1/Utils/pGFNFF/Src’
make: *** [makefile:274: …/…/Utils/pGFNFF/Src//libpGFNFF.a] Error 2
mv: cannot stat ‘gulp’: No such file or directory].
I followed your advice regarding these errors and edited mkgulp but now I keep getting ongoing syntax errors such as " unexpected ‘;;’". Any advice is highly appreciated.
Regards,
I’m afraid I’m not sure what’s going on - all I can guess is that when you deleted the -fallow-argument-mismatch option then you must have deleted too much from the line (e.g. delete to the end of the line) and corrupted the mkgulp file. I’ll try to attach a version of mkgulp where I’ve just removed this option to see if it helps you. Of course the other option is to updated your gfortran compiler to at least version 10, if not version 11, as this option will then be present and required.
Regards,
I gave it a try on both my laptop and cluster but got this error:
gfortran: error: csignal.o: No such file or directory
make: *** [makefile:221: gulp] Error 1
mv: cannot stat ‘gulp’: No such file or directory
Any advice is highly appreciated.
Hi Sama,
Sorry for the hiccup - RUNCC was missing from the gfortran serial setup. I’ll attach a version with the extra line (or you can type “gfortran -c csignal.c” and move the csignal.o to the sub-directory with all the other .o files). I’ve also added the mkgulp_old_gfortran file to the tarfile for 6.1 so that users can just copy a file rather than edit a line in mkgulp.
Regards,
Julian
I tried to install gulp using this version of mkgulp_old_gfortran (renamed to mkgulp) and I’m getting errors about “undefined reference”. With the final line of error being: “collect2: error: ld returned 1 exit status
make: *** [makefile:222: gulp] Error 1
mv: cannot stat ‘gulp’: No such file or directory”
Hi Molly,
The key thing is to look and see what is “undefined” in the error messages. My guess would be the maths libraries which can be set by commenting/uncommenting the MLIB lines in the mkgulp file depending on whether you have installed optimised maths libraries or not. In the latest tar file for 6.1 I’ve set the default to be source compiled lapack/blas so that things will work for those who are not comfortable with editing the mkgulp file, though the use of optimised maths libraries is recommend if available. I’ll attach more versions of mkgulp with the change here.
Regards,
Julian mkgulp (11.5 KB) mkgulp_old_gfortran (11.4 KB)
Hi Julian,
Thanks for that, the new file worked.
I’ve now got an issue with setting the environmental variables. I’ve added the environment variables into the .bashrc file in addition to the .profile file, and I am able to run GULP optimisations within the wsl terminal successfully. However, these environments don’t seem to follow across to jupyter notebook (even when launched from the same shell) as I am getting an error which indicates that I am unable to generate a gulp_opt.xyz file. the gulp_opt.ginout file which is generated is blank.
I also have tried defining the environments within the workbook but am getting the same error.
Hi Molly,
I think you may need to post this one to a forum for jupyter notebooks since it seems to be an issue with how these work rather than GULP if it runs fine outside of the notebook. GULP shouldn’t need the environment variables set to work if you place everything you need in the local directory.
Best regards,
Julian
I just downloaded GULP today and it still uses the framework accelerate flag by default. On line 227 of mkgulp I deleted it like you suggested, but why is the makefile not checking which os before executing the build command? On line 120 the mkgulp gets the os name. I guess I’m a little confused as if mkgulp is just a little weird or if I’m doing something wrong.
I’m not sure which tar file you’ve download? When I look in my repository it seems that accelerate is commented for 6.1 (i.e. the latest version). As for checking os, I’ve thought about it, but I’m a fortran programmer rather than a scripting expert & so there may have been issues when I tried to add this in. I guess a bit of experience with vi is good for users & in parallel or with optimised maths libraries there will always be some changes necessary.
Of course for users that don’t what to get their hands dirty with compilation they can obtain an executable from Biovia as part of Materials Studio to make their life easy.
I am using GULP 6.1.2 which I think is the newest. I attached the mkgulp file that it came with. I think Line 227 is what we’re talking about. At least its the line I edited to fix it.
Thanks for clarifying. If you download 6.1 (which is more recent) then the accelerate has been removed by default. The reason for 6.1.1 / 6.1.2 (as well as the latest 6.1 version) is that there is a building tool EasyBuild (which is a bit of a cross-post) that requires fixed tar files with a known checksum & so once these tar files are released they can’t be changed. For those not using EasyBuild then it’s best to use 6.1.
Not sure what happened with 6.1 as the code repository has it removed. Unfortunately I’m still waiting for our IT people to re-enable access for me to upload new versions and so I can’t currently fix it - sorry. For 6.1.2 it can’t be changed since this would mess up the checksum for EasyBuild and so it would have to be fixed in a 6.1.3 version.
Not a problem! Just wanted to let you know (or at least, I think that’s the case). I used the custom file you posted earlier in this thread, which worked great in the meantime! Thanks.
I am trying to install gulp6.0 to my mac (again) but now I have the following error when I type in ./mkgulp. Do you know how I can fix this? Thank you very much for your help.
Best,
Jack
ld: unsupported tapi file type ‘!tapi-tbd’ in YAML file ‘/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/lib/libSystem.tbd’ for architecture x86_64
