Something like: ln -s path/to/libcudart.8.0.dylib path/to/libcudart.7.5.dylib
You may need to do ldd to find additional libraries that need to be linked or find them with trial and error. This often works to get executables compiled with an older version of a library working, but Stam may know that CUDA 8.0 will not work for some other reason. Peace, Matt. From: "Kim, Sang-Young" <sak...@pitt.edu<mailto:sak...@pitt.edu>> Date: Tuesday, August 22, 2017 at 3:28 PM To: Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk<mailto:stamatios.sotiropou...@ndcn.ox.ac.uk>>, Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] dMRI: Error while running "run_eddy.sh" I mean CUDA 7.5 is not compatible with Mac OSX 10.12.5. So I cannot install CUDA 7.5 on my Mac. Please see below: New Release 7.5.21 * CUDA 7.5 support * Supported MAC OS X 10.11.x 10.10.x 10.9.x Matt, how and where should I make symlink? I have no idea how to do it. I’m sorry for bothering you. Thank you both. Sang-Young On Aug 22, 2017, at 4:20 PM, Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk<mailto:stamatios.sotiropou...@ndcn.ox.ac.uk>> wrote: Eddy_cuda is compiled with 7.5, so you need CUDA 7.5. In most systems you can have more than one CUDA installations. Are you sure you cannot have CUDA 7.5 installed after installing CUDA 8.0? You could then link to the appropriate directory. Cheers Stam On 22 Aug 2017, at 21:01, Kim, Sang-Young <sak...@pitt.edu<mailto:sak...@pitt.edu>> wrote: Dear Stam: I tried to download CUDA 7.5. But my Mac version is 10.12.5, which is not compatible with CUDA 7.5. So I downloaded CUDA 8.0. After installing the CUDA 8.0 and setting the path in the .bash_profile, I ran "eddy_cuda". Unfortunately, the same error came up. It looks like "eddy_cuda" cannot be run on the most recent version of Mac because of CUDA incompatibility. Do you have any other idea to solve this issue? Thanks. Sang-Young On Aug 22, 2017, at 3:49 PM, Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk<mailto:stamatios.sotiropou...@ndcn.ox.ac.uk>> wrote: Hi you need to install CUDA 7.5 and have LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib64 export LD_LIBRARY_PATH in your ~/.bashrc, assuming that /usr/local/cuda is where you have installed CUDA, otherwise replace accordingly. Cheers Stam On 22 Aug 2017, at 20:01, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Actually that looks like a cuda library error and your pipeline setup looks fine. You might ask on the FSL list about that. Peace, Matt. From: "Kim, Sang-Young" <sak...@pitt.edu<mailto:sak...@pitt.edu>> Date: Tuesday, August 22, 2017 at 1:55 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] dMRI: Error while running "run_eddy.sh" I’m sorry for misunderstanding. Yes, the Pipelines is in the ${HOME}/projects/Pipelines. The other pipelines such as PreFreeSurferPipeline, FreeSurferPipeline, PostFreeSurferPipeline, fMRIVolumePipeline and fMRISurfacePipeline can be run successfully without any errors. The followings are the variables in the DiffusionPreprocessingBatch script. ************************************************************************************* StudyFolder="/Volumes/LaCieMac3TB/HIV_HCP_pipeline/Data" Subjlist="30067" EnvironmentScript="${HOME}/projects/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh" SubjectID="$Subject" RawDataDir="$StudyFolder/$SubjectID/unprocessed/3T/Diffusion" PosData="${RawDataDir}/${SubjectID}_3T_DWI_dir113_AP.nii.gz" NegData="${RawDataDir}/${SubjectID}_3T_DWI_dir113_PA.nii.gz" EchoSpacing=0.77 PEdir=2 Gdcoeffs="${HCPPIPEDIR_Config}/coeff_AS82_Prisma.grad" ************************************************************************************* Thanks. Sang-Young On Aug 22, 2017, at 2:44 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: I mean the launcher script not the environment script. Although is that really where you have ${HCPIPEDIR}? Peace, Matt. From: "Kim, Sang-Young" <sak...@pitt.edu<mailto:sak...@pitt.edu>> Date: Tuesday, August 22, 2017 at 1:42 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] dMRI: Error while running "run_eddy.sh" The followings are the variables in SetUpHCPPipeline.sh. *************************************************** export FSL_DIR=${FSLDIR} # Set up FreeSurfer (if not already done so in the running environment) # Uncomment the following 2 lines (remove the leading #) and correct the FREESURFER_HOME setting for your setup export FREESURFER_HOME=/Applications/freesurfer source ${FREESURFER_HOME}/SetUpFreeSurfer.sh > /dev/null 2>&1 # Set up specific environment variables for the HCP Pipeline export HCPPIPEDIR=${HOME}/projects/Pipelines export CARET7DIR=/Applications/workbench/bin_macosx64 export MSMCONFIGDIR=${HCPPIPEDIR}/MSMConfig export MATLAB_COMPILER_RUNTIME=/Applications/MATLAB/MATLAB_Runtime/v91 export FSL_FIXDIR=/usr/local/fix export MSMBin=${HCPPIPEDIR}/MSMBinaries export HCPPIPEDIR_Templates=${HCPPIPEDIR}/global/templates export HCPPIPEDIR_Bin=${HCPPIPEDIR}/global/binaries export HCPPIPEDIR_Config=${HCPPIPEDIR}/global/config export HCPPIPEDIR_PreFS=${HCPPIPEDIR}/PreFreeSurfer/scripts export HCPPIPEDIR_FS=${HCPPIPEDIR}/FreeSurfer/scripts export HCPPIPEDIR_PostFS=${HCPPIPEDIR}/PostFreeSurfer/scripts export HCPPIPEDIR_fMRISurf=${HCPPIPEDIR}/fMRISurface/scripts export HCPPIPEDIR_fMRIVol=${HCPPIPEDIR}/fMRIVolume/scripts export HCPPIPEDIR_tfMRI=${HCPPIPEDIR}/tfMRI/scripts export HCPPIPEDIR_dMRI=${HCPPIPEDIR}/DiffusionPreprocessing/scripts export HCPPIPEDIR_dMRITract=${HCPPIPEDIR}/DiffusionTractography/scripts export HCPPIPEDIR_Global=${HCPPIPEDIR}/global/scripts export HCPPIPEDIR_tfMRIAnalysis=${HCPPIPEDIR}/TaskfMRIAnalysis/scripts ************************************************************** Thanks. Sang-Young On Aug 22, 2017, at 2:38 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Need to know the variables in the laugher script. Peace, Matt. On 8/22/17, 1:35 PM, "Kim, Sang-Young" <sak...@pitt.edu<mailto:sak...@pitt.edu>> wrote: Dear Matt: Since I have added path for batch scripts, I just ran the pipeline in the terminal as follow: DiffusionPreprocessingBatch.sh I believe all environment variables are correctly set in "SetUpHCPPipeline.sh". Thanks. Sang-Young On Aug 22, 2017, at 2:28 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: How did you call the pipeline? Peace, Matt. On 8/22/17, 10:57 AM, "hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> on behalf of Kim, Sang-Young" <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> on behalf of sak...@pitt.edu<mailto:sak...@pitt.edu>> wrote: Dear HCP experts: We have diffusion MRI data acquired from Siemens Prisma 3 T scanner. The dMRI data were acquired with 113 diffusion direction and AP phase encoding. The b0 images were acquired with opposite phase encoding direction for topup. I would like to preprocess dMRI data using DiffusionPreprocessing pipeline provided from HCP. So I ran the DiffusionPreprocessingBatch.sh file with minor modification for scan setting and gradient nonlinearity correction. But error message came up while running "run_eddy.sh". Please see below: **************************************************************** dyld: Library not loaded: @rpath/libcudart.7.5.dylib Referenced from: /usr/local/fsl/bin/eddy_cuda Reason: image not found /Users/sang-young/projects/Pipelines/DiffusionPreprocessing/scripts/run_ ed dy.sh: line 380: 16731 Abort trap: 6 ${eddy_command} ****************************************************************** Does anybody have similar problem? Any insights would be greatly appreciated. Thanks in advance. Sang-Young Kim, Ph.D. Postdoctoral Research Fellow Department of Radiology, University of Pittsburgh _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.humanconnectome.org%2Fmailman%2Flistinfo%2Fhcp-users&data=01%7C01%7CSAK245%40pitt.edu%7C1fff63211db045e98a0b08d4e996f468%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=ptm%2FYVFt3TcCj%2B1%2F9sN2%2B34Fw3Q4SeTLw4cMyh9sNoE%3D&reserved=0> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.humanconnectome.org%2Fmailman%2Flistinfo%2Fhcp-users&data=01%7C01%7CSAK245%40pitt.edu%7C1fff63211db045e98a0b08d4e996f468%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=ptm%2FYVFt3TcCj%2B1%2F9sN2%2B34Fw3Q4SeTLw4cMyh9sNoE%3D&reserved=0> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.humanconnectome.org%2Fmailman%2Flistinfo%2Fhcp-users&data=01%7C01%7CSAK245%40pitt.edu%7C1fff63211db045e98a0b08d4e996f468%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=ptm%2FYVFt3TcCj%2B1%2F9sN2%2B34Fw3Q4SeTLw4cMyh9sNoE%3D&reserved=0> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.humanconnectome.org%2Fmailman%2Flistinfo%2Fhcp-users&data=01%7C01%7CSAK245%40pitt.edu%7C1fff63211db045e98a0b08d4e996f468%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=ptm%2FYVFt3TcCj%2B1%2F9sN2%2B34Fw3Q4SeTLw4cMyh9sNoE%3D&reserved=0> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
