Hi Ali,
Can you please remove the MCR directory and install it using the instructions
found at https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime? I think this
will fix the issue.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Snedden, Ali
<ali.sned...@nationwidechildrens.org>
Date: Wednesday, January 27, 2021 at 11:46 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Java / Matlab Runtime error
External Email - Use Caution
Hello,
I’m helping a user run freesurfer/7.1.0 on CentOS 8.1. They initially
encountered an error due to the missing Matlab Compiler Runtime (MCR). I
downloaded the package and installed it in the location suggested by the error
message :
LINUX:
cd /gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download
curl
"https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2014bLinux.tar.gz";
-o "runtime2014b.tar.gz"
tar xvf runtime2014b.tar.gz
After installing the MCR, I had to change all the subdirectories’ in MCRv84 to
755 permissions so our user could access it. When trying to run
`segmentHA_T1.sh`, she gets the error :
[user@computer-name Subjects]$ export
FS_LICENSE=/gpfs0/home1/group/lab/Software/FreeSurfer/license.txt
[user@computer-name Subjects]$ export
SUBJECTS_DIR=/gpfs0/home1/group/lab/DATA/ANALYSES/Test/FreeSurfer7/Subjects
[user@computer-name Subjects]$ cd
/gpfs0/home1/group/lab/DATA/ANALYSES/Test/FreeSurfer7/Subjects
[user@computer-name Subjects]$ segmentHA_T1.sh subject1
#--------------------------------------------
#@# Hippocampal Subfields processing (T1) left Wed Jan 27 10:53:02 EST 2021
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is
.:/lib64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//runtime/glnxa64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//bin/glnxa64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/os/glnxa64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/lib:/gpfs0/export/apps/easybuild/software/binutils/2.34-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/zlib/1.2.11-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/GCCcore/9.3.0/lib64:/gpfs0/export/apps/easybuild/software/GCCcore/9.3.0/lib
Error using checkRequiredMCRProducts (line 25)
Java exception occurred:
java.lang.NullPointerException
at
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)
at
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)
at
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)
at
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)
at
com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)
Error in deployrc (line 9)
Error in matlabrc (line 238)
Command exited with non-zero status 255
@#@FSTIME 2021:01:27:10:53:02 run_segmentSubjectT1_autoEstimateAlveusML.sh N
13 e 35.91 S 0.42 U 2.80 P 8% M 184232 F 0 R 52021 W 0 c 11 w 7851 I 0 O 84128
L 0.02 0.06 0.08
@#@FSLOADPOST 2021:01:27:10:53:38 run_segmentSubjectT1_autoEstimateAlveusML.sh
N 13 0.35 0.15 0.11
Linux computer-name 4.18.0-147.el8.x86_64 #1 SMP Wed Dec 4 21:51:45 UTC 2019
x86_64 x86_64 x86_64 GNU/Linux
T1 hippocampal subfields exited with ERRORS at Wed Jan 27 10:53:38 EST 2021
For more details, see the log file
/gpfs0/home1/group/lab/DATA/ANALYSES/Test/FreeSurfer7/Subjects/subject1/scripts/hippocampal-subfields-T1.log
In the archive, it seems that this has been encountered before
(here<https://secure-web.cisco.com/19si_oaGGE_Rf_ZxUuvB_adcHrxJiJjhP5iL5nhhr9Xa79-fy1G5fztuCyCFq6TvmDT-RftRgx8r3K206bDoNBtrUbc7KcojbRexJySrgg5wN-dvaj0EkbZJaiyykuHFXwKzwiAGAO8lG6d0Dj2jy94-KktwBPefan2fqunI59ga3Vz_Fc-fEZheuCIWneoI00o0S6ZDsRaWjhhziLl3IILVg3Xu4QfbBBvIfX6QEXB7Yz_hW_mJ8ABzuTKUk96ecyogdL9wILWgL4lxQNbo7sg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg64018.html>
and
there<https://secure-web.cisco.com/13EvbbtOVHHlv-B8zjJFgKM0MEuIpwNHOsMVGI6vp_BOjF3tta7VWeqrdfHb-o8zmvqI5Dd36AkLsyEJac2ZZRE_ua6FsPElMfNK09PSps0ty8V7XAkeRrdGIFqgs52CxevFZbv2QJotk1qPnTvEdCgveMGIulR829uQ8eXB0aNomXqDXRmZz7_IKPkIJxFx1rUBEBYR06mr9lBqWGuyqUaHFWoWdWukaNGKM_P0r-r8jTg4MhFIcQLIRY3bG-a39OPP1OAezi8DJfxU3lYhM_A/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dsubject%3A%2522Re%255C%253A%2B%255C%255BFreesurfer%255C%255D%2BFS6.0%255C-dev%2B%255C%2528Jun27%252C%2B2018%255C%2529%2BHippocampal%2Bsubfield%2BMatlab%2Bruntime%2BJava%2Berror%2522%26o%3Dnewest%26f%3D1>).
Unfortunately the only solution is to ‘fix the permissions’ without
specifying which files and to what permissions.
Question:
1. Is there any resolution to this issue?
2. Is the Matlab 2014b compatible with CentOS 8.1?
Best regards,
======================================
Ali Snedden, Ph.D.
HPC Scientific Programmer
The High Performance Computing Facility
Abigail Wexner Research Institute at Nationwide Children’s Hospital
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