msm on ubuntu 16.04 - Githubissues

ecr05 / MSM_HOCR

Multimodal Surface Matching with Higher order Clique Reduction: Mac OS and Linux binaries

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msm on ubuntu 16.04 #10

Closed jcupitt closed 3 years ago

jcupitt commented 4 years ago

Hello, I've made a Dockerfile that builds MSM from source on Ubuntu 16.04, perhaps it could be useful:

https://github.com/jcupitt/docker-builds/blob/master/msm-fsl6-ubuntu16.04/Dockerfile

I had to make a few small changes to FSL to get it to work with Ubuntu 16.04, and also change the libs list for MSM itself:

https://github.com/ecr05/MSM_HOCR/commit/a74ada542b9845ddbe1758a8f276e4e3496c4dd3

There's probably a better way to get it to link, of course.

jcupitt commented 4 years ago

The Dockerfile has comments in, but the process is:

Ubuntu 16.04 is not supported by the FSL6 makefiles.
I made a config for it from linux_64-gcc4.8 (to make gnu_64-gcc4.8).
That has -lopenblas in LIB_NEWMAT (incorrectly, I think), but that ends up USRLDFLAGS in MSM, so it won't link since it'll come before the object that needs the library.
I added -lopenblas to the end of the MSM link line to fix this.
-lopenblas in turn needs libgfortran.so.3, but FSL is missing a symlink for libgfortran.so, so -lgfortran won't work.
I added the symlink to FSL, but another fix would be to append /usr/local/fsl/lib/libgfortran.so.3 to the MSM link line.

ShacharGal commented 4 years ago

were also having some trouble compiling MSM on ubuntu 18.04, with an error regarding newmat: /usr/local/fsl/include/utils/log.h:85:10: fatal error: newmatap.h: No such file or directory

you think this process could work for us as well?

jcupitt commented 4 years ago

Yes, it should work. I've updated it to use FSL 6.0.1, which is quite a bit better.

ShacharGal commented 4 years ago

im using fsl 6.0.0 would it be a problem?

ecr05 commented 4 years ago

Unfortunately FSL is changing rapidly in the backend at the moment. I don't know that this is the same problem. Try it and if it doesn't work post to FSL list and I will try and help you fix it with their support.

jcupitt commented 4 years ago

An older version of that docker script worked for 6.0.0, the current version is updated for 6.0.2.

Old 6.0.0 build:

https://github.com/jcupitt/docker-builds/tree/549b050a1e18f022cfe187b28cc4293a04202a78/msm-fsl6-ubuntu16.04

The current one works for 6.0.2, I built it myself yesterday.

ShacharGal commented 4 years ago

we got this error:

/bin/sh: 1: cannot open /usr/local/src/fsl/fsl.sh.patch: No such file The command '/bin/sh -c cd $fsl_prefix/etc/fslconf && patch < /usr/local/src/fsl/fsl.sh.patch' returned a non-zero code: 2

do you know where i can get fsl.sh.patch?

ecr05 commented 4 years ago

Really you need to post these questions to the FSL list. I do not know the answer but they will.

ecr05 commented 4 years ago

Incidentally - wont the binaries from the release tab work for you?

ShacharGal commented 4 years ago

indeed it does. i didnt know it was an option....

thanks