{bio}[system/system] FreeSurfer v8.1.0 w/ rocky9_x86_64 by pavelToman · Pull Request #25342 · easybuilders/easybuild-easyconfigs

pavelToman · 2026-02-19T16:17:20Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#640

github-actions · 2026-02-19T16:17:51Z

Updated software `FreeSurfer-8.1.0-rocky9_x86_64.eb`

Diff against FreeSurfer-7.4.1-ubuntu22_amd64.eb

easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-ubuntu22_amd64.eb

diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-ubuntu22_amd64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-8.1.0-rocky9_x86_64.eb
index 3c9330102f..51dcb1582b 100644
--- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-ubuntu22_amd64.eb
+++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-8.1.0-rocky9_x86_64.eb
@@ -1,6 +1,6 @@
 name = 'FreeSurfer'
-version = '7.4.1'
-versionsuffix = '-ubuntu22_amd64'
+version = '8.1.0'
+versionsuffix = '-rocky9_x86_64'
 
 homepage = 'https://surfer.nmr.mgh.harvard.edu/'
 description = """FreeSurfer is a set of tools for analysis and visualization
@@ -12,12 +12,9 @@ toolchain = SYSTEM
 
 source_urls = ['https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/']
 sources = ['%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz']
-patches = ['%(namelower)s-%(version)s-hardcoded-path.patch']
-checksums = [
-    {'freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz':
-     '6db470445f3b2e973fcfdc9231c775896e54a4dbfc4ce0d5ef5775bc7dca182d'},
-    {'freesurfer-7.4.1-hardcoded-path.patch': 'f75d8eeb90086d290b8122c5174b77c210ea5d900bdc3040736aef4d69e65295'},
-]
+checksums = ['6158acc772fcbb5220c89e6405e8b56e4618701b13b6bbe6e8da77695f5e5546']
+
+osdependencies = ['tcsh']
 
 dependencies = [('MCR', 'R2019b.8')]
 
@@ -25,6 +22,11 @@ postinstallcmds = ["ln -s $EBROOTMCR/v97 %(installdir)s/MCRv97"]
 
 license_text = """email@example.com
 00000
-g1bb3r1sh"""
+g1bb3r1sh
+"""
+
+# Prepend system libs so FreeSurfer binaries pick up the system libstdc++.so.6 first.
+# This avoids GLIBCXX_* symbol errors caused by the older libstdc++ bundled with MCR.
+modextrapaths = {'LD_LIBRARY_PATH': ['/usr/lib64']}
 
 moduleclass = 'bio'

Diff against FreeSurfer-7.4.1-ubuntu20_amd64.eb

easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-ubuntu20_amd64.eb

diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-ubuntu20_amd64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-8.1.0-rocky9_x86_64.eb
index 5e686cd301..51dcb1582b 100644
--- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-ubuntu20_amd64.eb
+++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-8.1.0-rocky9_x86_64.eb
@@ -1,6 +1,6 @@
 name = 'FreeSurfer'
-version = '7.4.1'
-versionsuffix = '-ubuntu20_amd64'
+version = '8.1.0'
+versionsuffix = '-rocky9_x86_64'
 
 homepage = 'https://surfer.nmr.mgh.harvard.edu/'
 description = """FreeSurfer is a set of tools for analysis and visualization
@@ -12,12 +12,9 @@ toolchain = SYSTEM
 
 source_urls = ['https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/']
 sources = ['%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz']
-patches = ['%(namelower)s-%(version)s-hardcoded-path.patch']
-checksums = [
-    {'freesurfer-linux-ubuntu20_amd64-7.4.1.tar.gz':
-     'f61ab4bf6594f996e1a664eb00ab60fb731b7642751bacd4f32a915820a1d7c8'},
-    {'freesurfer-7.4.1-hardcoded-path.patch': 'f75d8eeb90086d290b8122c5174b77c210ea5d900bdc3040736aef4d69e65295'},
-]
+checksums = ['6158acc772fcbb5220c89e6405e8b56e4618701b13b6bbe6e8da77695f5e5546']
+
+osdependencies = ['tcsh']
 
 dependencies = [('MCR', 'R2019b.8')]
 
@@ -25,6 +22,11 @@ postinstallcmds = ["ln -s $EBROOTMCR/v97 %(installdir)s/MCRv97"]
 
 license_text = """email@example.com
 00000
-g1bb3r1sh"""
+g1bb3r1sh
+"""
+
+# Prepend system libs so FreeSurfer binaries pick up the system libstdc++.so.6 first.
+# This avoids GLIBCXX_* symbol errors caused by the older libstdc++ bundled with MCR.
+modextrapaths = {'LD_LIBRARY_PATH': ['/usr/lib64']}
 
 moduleclass = 'bio'

Diff against FreeSurfer-7.4.1-centos8_x86_64.eb

easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-centos8_x86_64.eb

diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-centos8_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-8.1.0-rocky9_x86_64.eb
index 4499112638..51dcb1582b 100644
--- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-centos8_x86_64.eb
+++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-8.1.0-rocky9_x86_64.eb
@@ -1,6 +1,6 @@
 name = 'FreeSurfer'
-version = '7.4.1'
-versionsuffix = '-centos8_x86_64'
+version = '8.1.0'
+versionsuffix = '-rocky9_x86_64'
 
 homepage = 'https://surfer.nmr.mgh.harvard.edu/'
 description = """FreeSurfer is a set of tools for analysis and visualization
@@ -12,12 +12,9 @@ toolchain = SYSTEM
 
 source_urls = ['https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/']
 sources = ['%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz']
-patches = ['%(namelower)s-%(version)s-hardcoded-path.patch']
-checksums = [
-    {'freesurfer-linux-centos8_x86_64-7.4.1.tar.gz':
-     '302f2745886fcb571f2050bc2e2a7b4ff982e844bcc20c842d0d0b32b514c56a'},
-    {'freesurfer-7.4.1-hardcoded-path.patch': 'f75d8eeb90086d290b8122c5174b77c210ea5d900bdc3040736aef4d69e65295'},
-]
+checksums = ['6158acc772fcbb5220c89e6405e8b56e4618701b13b6bbe6e8da77695f5e5546']
+
+osdependencies = ['tcsh']
 
 dependencies = [('MCR', 'R2019b.8')]
 
@@ -25,6 +22,11 @@ postinstallcmds = ["ln -s $EBROOTMCR/v97 %(installdir)s/MCRv97"]
 
 license_text = """email@example.com
 00000
-g1bb3r1sh"""
+g1bb3r1sh
+"""
+
+# Prepend system libs so FreeSurfer binaries pick up the system libstdc++.so.6 first.
+# This avoids GLIBCXX_* symbol errors caused by the older libstdc++ bundled with MCR.
+modextrapaths = {'LD_LIBRARY_PATH': ['/usr/lib64']}
 
 moduleclass = 'bio'

pavelToman · 2026-02-19T16:19:01Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-02-19T16:20:08Z

@pavelToman: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=25342 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25342 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9770

Test results coming soon (I hope)...

Details

- notification for comment with ID 3928304488 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

pavelToman · 2026-02-19T16:25:09Z

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (total: 5 mins 42 secs) (1 easyconfigs in total)
node4010.donphan.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 580.95.05, Python 3.9.21
See https://gist.github.com/pavelToman/67564945596f6e88c617e590e27502ae for a full test report.

pavelToman · 2026-02-19T16:30:28Z

Test report by @pavelToman
SUCCESS
Build succeeded for 2 out of 2 (total: 10 mins 38 secs) (1 easyconfigs in total)
node4231.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.21
See https://gist.github.com/pavelToman/37d3e5183bc2e43fb3e292b9ce691369 for a full test report.

verdurin · 2026-02-19T19:46:32Z

Test report by @verdurin
FAILED
Build succeeded for 1 out of 2 (total: 2 hours 56 mins 46 secs) (1 easyconfigs in total)
centos-stream-9 - Linux CentOS Stream 9, x86_64, Intel Core Processor (Skylake, IBRS), Python 3.12.12
See https://gist.github.com/verdurin/d66db695638e2b27fe219aa89e6bd761 for a full test report.

boegelbot · 2026-02-19T20:46:23Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (total: 4 hours 25 mins 56 secs) (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/4159a1caa2141b48cb635e659c6c570b for a full test report.

verdurin · 2026-02-20T09:40:46Z

@pavelToman my build failed because the build node didn't have Tcsh installed. That ought to be either a dependency or an OS dependency (preferably the former).

pavelToman · 2026-02-20T10:24:57Z

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (total: 5 mins 48 secs) (1 easyconfigs in total)
node4010.donphan.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 580.95.05, Python 3.9.21
See https://gist.github.com/pavelToman/d21fb7c56a511e8535837fe89f2ea5be for a full test report.

JarneRenders · 2026-02-20T15:37:45Z

This builds fine for me, but trying a run with some tutorialdata fails with a missing liblapack.so.3.

$ recon-all -i dicom_challenge/dicoms/I0 -subject test
Adding options -fix-ento-wm -transfer-base-bfs -fix-vsinus -fix-mca-dura -fix-ga -fix-acj -synthstrip -synthseg -synthmorph
fs-check-version --s test --o /tmp/tmp.0LSoec
Fri Feb 20 16:34:37 CET 2026

setenv SUBJECTS_DIR /rhea/scratch/brussel/vo/000/bvo00005/vsc11353/easybuild/install/zen5/software/FreeSurfer/8.1.0-rocky9_x86_64/subjects
cd /rhea/scratch/brussel/vo/000/bvo00005/vsc11353/myeasyconfigs/freesurfer/tutorial_data_20190918_1558
/scratch/brussel/vo/000/bvo00005/vsc11353/easybuild/install/zen5/software/FreeSurfer/8.1.0-rocky9_x86_64/bin/fs-check-version --s test --o /tmp/tmp.0LSoec
-rwxr-xr-x+ 1 vsc11353 vsc11353 18565 Feb  5 04:28 /scratch/brussel/vo/000/bvo00005/vsc11353/easybuild/install/zen5/software/FreeSurfer/8.1.0-rocky9_x86_64/bin/fs-check-version

freesurfer-linux-rocky9_x86_64-8.1.0-20260204-f30dfed
$Id$
Linux node510.anansi.os 5.14.0-611.16.1.el9_7.x86_64 #1 SMP PREEMPT_DYNAMIC Mon Dec 22 12:21:56 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
pid 3437361
Current FS Version freesurfer-linux-rocky9_x86_64-8.1.0-20260204-f30dfed
Subject does not have a bstampfile, copying /scratch/brussel/vo/000/bvo00005/vsc11353/easybuild/install/zen5/software/FreeSurfer/8.1.0-rocky9_x86_64/build-stamp.txt
Subject FS Version: freesurfer-linux-rocky9_x86_64-8.1.0-20260204-f30dfed
No constraints on version because REQ=UnSet and FsVerFile=NotThere
#@#% fs-check-version match = 1
fs-check-version Done
INFO: SUBJECTS_DIR is /rhea/scratch/brussel/vo/000/bvo00005/vsc11353/easybuild/install/zen5/software/FreeSurfer/8.1.0-rocky9_x86_64/subjects
Actual FREESURFER_HOME /rhea/scratch/brussel/vo/000/bvo00005/vsc11353/easybuild/install/zen5/software/FreeSurfer/8.1.0-rocky9_x86_64
Linux node510.anansi.os 5.14.0-611.16.1.el9_7.x86_64 #1 SMP PREEMPT_DYNAMIC Mon Dec 22 12:21:56 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
mri_robust_register: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
ERROR: Executable 'mri_robust_register -all-info failed! Is it missing from the distribution?'

pavelToman · 2026-02-20T17:15:22Z

I check this:
ldd $FREESURFER_HOME/bin/mri_robust_register returns:

liblapack.so.3 => not found
libblas.so.3 => not found

adding easyconfigs: FreeSurfer-8.1.0-rocky9_x86_64.eb

e59b6fb

pavelToman added the update label Feb 19, 2026

pavelToman mentioned this pull request Feb 19, 2026

FreeSurfer 7.4.1 and FSL 6.0.7.11 vscentrum/vsc-software-stack#640

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{bio}[system/system] FreeSurfer v8.1.0 w/ rocky9_x86_64#25342

{bio}[system/system] FreeSurfer v8.1.0 w/ rocky9_x86_64#25342
pavelToman wants to merge 2 commits intoeasybuilders:developfrom
pavelToman:20260219171717_new_pr_FreeSurfer810

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Updated software `FreeSurfer-8.1.0-rocky9_x86_64.eb`

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