search

ecr05 / MSM_HOCR

Multimodal Surface Matching with Higher order Clique Reduction: Mac OS and Linux binaries
35 stars 10 forks source link

niftiio, fslio not found #8

Closed tashrifbillah closed 4 years ago

tashrifbillah commented 5 years ago

Hey guys,

We are getting the above libraries missing error:

[~/Downloads/MSM_HOCR/src/MSM]$ make install
make[1]: Entering directory `/rfanfs/pnl-zorro/projects/U01_HCP_Psychosis/HCPPipeline/MSM_HOCR/src/MSM'
make[2]: Entering directory `/rfanfs/pnl-zorro/projects/U01_HCP_Psychosis/HCPPipeline/MSM_HOCR/src/MSM'
c++ -Wl,-rpath,'$ORIGIN/../lib' -L/rfanfs/pnl-zorro/software/pnlpipe3/fsl/extras/lib -lopenblas -L/rfanfs/pnl-zorro/software/pnlpipe3/fsl/extras/lib -L/lib64  -L/rfanfs/pnl-zorro/software/pnlpipe3/fsl/extras/lib -L/rfanfs/pnl-zorro/software/pnlpipe3/fsl/extras/lib -L/rfanfs/pnl-zorro/software/pnlpipe3/fsl/extras/lib -L/rfanfs/pnl-zorro/software/pnlpipe3/fsl/extras/lib -L/rfanfs/pnl-zorro/software/pnlpipe3/fsl/extras/lib   -L. -L/rfanfs/pnl-zorro/projects/U01_HCP_Psychosis/HCPPipeline/fsl_dev_dir/lib  -L/rfanfs/pnl-zorro/projects/U01_HCP_Psychosis/HCPPipeline/fsl_dev_dir/extras/lib -L/rfanfs/pnl-zorro/software/pnlpipe3/fsl/lib -L. -L/rfanfs/pnl-zorro/projects/U01_HCP_Psychosis/HCPPipeline/fsl_dev_dir/lib -L/rfanfs/pnl-zorro/software/pnlpipe3/fsl/lib -o msm msm.o -lmeshreg -lfastpd -ldiscrete -lnewmeshclass -lfslsurface -lgiftiio -lmm  -lexpat  -lfslvtkio -lnewimage  -lmiscmaths -lmiscplot -lmiscpic -lfslio -lniftiio -lnewmat -lutils  -lbint -lnewran -lprob -lznz -lgdc -lgd -lpng  -lz 
/usr/bin/ld: cannot find -lfslio
/usr/bin/ld: cannot find -lniftiio
collect2: error: ld returned 1 exit status
make[2]: *** [msm] Error 1
make[2]: Leaving directory `/rfanfs/pnl-zorro/projects/U01_HCP_Psychosis/HCPPipeline/MSM_HOCR/src/MSM'
make[1]: *** [master-install-script] Error 2
make[1]: Leaving directory `/rfanfs/pnl-zorro/projects/U01_HCP_Psychosis/HCPPipeline/MSM_HOCR/src/MSM'
make: *** [install] Error 2

Possible fix

Is this pipeline for FSL 5.0.11? In the stated version, we have both libfslio.a and libniftiio.a in ${FSLDIR}/lib, but those libraries probably have been removed in FSL 6.0.1. On the other hand, the prerequisites say FSL 6.0.1.

Even if the pipeline is for FSL 5.0.11, you don't have -L${FSLDIR}/lib in either of the USRINCFLAGS and USRLDFLAGS. For the compiler to be able to find them, we should link ${FSLDIR}/lib directory as well (similar for include).

ecr05 commented 5 years ago

Sorry - just seen this. Will get back to you asap

ecr05 commented 5 years ago

Should work now? Please let me know if you have any further problems

tashrifbillah commented 5 years ago

@ecr05

Should work now?

Are you referring to this commit ?

Can we keep the issue open until we get back to you?

ecr05 commented 5 years ago

Yes.

On Wed, 26 Jun 2019 at 16:17, Tashrif Billah notifications@github.com wrote:

@ecr05 https://github.com/ecr05

Should work now?

Are you referring to this commit https://github.com/ecr05/MSM_HOCR/commit/6e348e78d3003ce28b9ba2c2a8c7cadd773e713d ?

Can we keep the issue open until we get back to you?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ecr05/MSM_HOCR/issues/8?email_source=notifications&email_token=AD7GXPDOUCV2WP4WJDKAU7TP4OB7NA5CNFSM4HWYF252YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYT35NQ#issuecomment-505921206, or mute the thread https://github.com/notifications/unsubscribe-auth/AD7GXPFFDNDBZMWXDDEJXEDP4OB7NANCNFSM4HWYF25Q .

vanzod commented 4 years ago

@ecr05 I just built MSM from the master branch on top of FSL v6.0.1 and the build completed successfully. Thank you for taking care of this.

Would it be possible to have a release (I guess v3.0) from the current master ASAP?

ecr05 commented 4 years ago

Good point. I'll put it on my todo.

tashrifbillah commented 4 years ago

@vanzod , thanks for verifying the commit. Between the time I opened this issue and fix was given, my folks move on to other solution. So I didn't get a chance to test it.

@ecr05 feel free to close this issue.

ecr05 commented 4 years ago

@vanzod - sorry for the delay but just to let you know I have finally got round to building those binaries - thanks for the suggestion