External Email - Use Caution
Thank you. That seemed to work.
Best,
====================================== Ali Snedden, Ph.D. HPC Scientific Programmer The High Performance Computing Facility Abigail Wexner Research Institute at Nationwide Children’s Hospital
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Hoopes, Andrew" AHOOPES@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, January 27, 2021 at 12:30 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Java / Matlab Runtime error
Hi Ali,
Can you please remove the MCR directory and install it using the instructions found at https://secure-web.cisco.com/1q7ncSDiVmdcDnctxyRxdS9kfvzlqFQOUr2mbgA1_jcZ_ps...https://secure-web.cisco.com/1aQ1JL_davGdsj7PjO6BlRnaxg04WJ-LS2csZQb4UUpwC4zMeU6dFnm6ElVM6C86XbhJ5pLMl0Cf72_7u56Ii0hJvSF55co4e6ols7OK-8Y02mnynjqiBJxszYYkopduZixeIQRbUsww8QFnWiCecZr7jbGaJbXocsqYXIzS5I-JXQxxK1CiAAQ9Lql0bu1ZAt43KpZBXn86MDLRcGCoVptcYlGPsPZEeHGB912KnE7e-KZ8lyfbzZ-x1xKn7wQZWRRkiIK1o4rFqYyavUFWzCw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMatlabRuntime__%3B%21%21ODYTt7Uqo6LDP14%211RCpXwAPvW6lWWKt9R-ku2ObYruYDl-KqFLJvvOpgMcuQEXMhjpx-QM8j5wJ3vv0lF5g_LSNBnQ%24? I think this will fix the issue.
Best, Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Snedden, Ali Ali.Snedden@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://secure-web.cisco.com/13fqwuJ0h6N_rVfDgy4zeeSfP8PW_Zucrne8PLs-s210IBA..."https://secure-web.cisco.com/12fg_q2Z2ANsbb7Ptww7Z4aEcjmFodLwyk84-oiY-5QwyPr7-boA4Ske8Q4ERbDohGvFK-nxKqsUfeRddGaQTbTTtsVfi7SsnWNbb7B14KVJdHPiF2f0wyFMzXmj0aJsUKKWbJ8bET0inSP3z3wgjkIrlmlWmMdxP6AChy4a0kuCUBwqEQgWIoetzWj3lqO5gZbWU3HECgD-TJd26SXwi06ZzPNI9EBFvqBdOibeN_spQKdivNy1m1P8-jLqrahXvmN-a0wQwl-6hx-3QU0-WKA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMatlabRuntime%3Faction%3DAttachFile%26do%3Dget%26target%3Druntime2014bLinux.tar.gz%2A22__%3BJQ%21%21ODYTt7Uqo6LDP14%211RCpXwAPvW6lWWKt9R-ku2ObYruYDl-KqFLJvvOpgMcuQEXMhjpx-QM8j5wJ3vv0lF5gs7pyp38%24 -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 (herehttps://secure-web.cisco.com/13Rrk4VKAg12XFtc5SdBaCyFLuQnrsUWASWx4vhQPLsBPHPZaE8daMMs4B6WzDBMuNfnc3P-oXTzzpxf4KyvXRv1GoUwEGyQJw99-35F3OXiBdRl3m8gKSH5Wv_72f-jLZozo58Gj5eyBR2UDlXuPEWltWokLH8zSAbAuOMtyVuh7x44_poULjZmypi-b_2F02IxzADAiqNWfwIOZn8-jcPCWEvGV_JZZcHndE-X2OglefZCKq6lLGLvjgp7qXUaKTcVEON54eQos1SimXM432g/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F19si_oaGGE_Rf_ZxUuvB_adcHrxJiJjhP5iL5nhhr9Xa79-fy1G5fztuCyCFq6TvmDT-RftRgx8r3K206bDoNBtrUbc7KcojbRexJySrgg5wN-dvaj0EkbZJaiyykuHFXwKzwiAGAO8lG6d0Dj2jy94-KktwBPefan2fqunI59ga3Vz_Fc-fEZheuCIWneoI00o0S6ZDsRaWjhhziLl3IILVg3Xu4QfbBBvIfX6QEXB7Yz_hW_mJ8ABzuTKUk96ecyogdL9wILWgL4lxQNbo7sg%2Fhttps%2A3A%2A2F%2A2Fwww.mail-archive.com%2A2Ffreesurfer%2A40nmr.mgh.harvard.edu%2A2Fmsg64018.html__%3BJSUlJSUl%21%21ODYTt7Uqo6LDP14%211RCpXwAPvW6lWWKt9R-ku2ObYruYDl-KqFLJvvOpgMcuQEXMhjpx-QM8j5wJ3vv0lF5gzjvCLxM%24 and therehttps://secure-web.cisco.com/1Wvet5W4lNlADueS5IfQSLWQ1iZZgHk4dYGyuj_e4cd6w5Qf0-n0e11IsnO1qrq6H89kq2cXQY9cjbxy3OMmHdJ1poAfCsvosefOBcaTEqWGu9btK9p8USHvR70cWV8EfPDirHb1ZUkqpxToOtPMyOn_j8iBo1QUBmv_YGX_btO951eRhbp6QtyNI5ngmtgovtbIf5F4PwhcdN48gTTU5hKq6MZokeE3Kl033vZw8KK1PkHJ7nYbjwfn1LknxVzu6YjxR6zIJFmPvm0kQZe4cHg/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F13EvbbtOVHHlv-B8zjJFgKM0MEuIpwNHOsMVGI6vp_BOjF3tta7VWeqrdfHb-o8zmvqI5Dd36AkLsyEJac2ZZRE_ua6FsPElMfNK09PSps0ty8V7XAkeRrdGIFqgs52CxevFZbv2QJotk1qPnTvEdCgveMGIulR829uQ8eXB0aNomXqDXRmZz7_IKPkIJxFx1rUBEBYR06mr9lBqWGuyqUaHFWoWdWukaNGKM_P0r-r8jTg4MhFIcQLIRY3bG-a39OPP1OAezi8DJfxU3lYhM_A%2Fhttps%2A3A%2A2F%2A2Fwww.mail-archive.com%2A2Fsearch%2A3Fl%2A3Dfreesurfer%2A40nmr.mgh.harvard.edu%2A26q%2A3Dsubject%2A3A%2A2522Re%2A255C%2A253A%2A2B%2A255C%2A255BFreesurfer%2A255C%2A255D%2A2BFS6.0%2A255C-dev%2A2B%2A255C%2A2528Jun27%2A252C%2A2B2018%2A255C%2A2529%2A2BHippocampal%2A2Bsubfield%2A2BMatlab%2A2Bruntime%2A2BJava%2A2Berror%2A2522%2A26o%2A3Dnewest%2A26f%2A3D1__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU%21%21ODYTt7Uqo6LDP14%211RCpXwAPvW6lWWKt9R-ku2ObYruYDl-KqFLJvvOpgMcuQEXMhjpx-QM8j5wJ3vv0lF5gkJflTNs%24). 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