Possibility to add conn-toolbox

[fphsFischmeister]

Thanks for this excellent tool!

We want to set up neurodesk vnm's for our students to run their analysis remotely on our server.
We are mostly using SPM and the CONN toolbox right now and thus wanted to ask how the latter can be implemented? I would be happy to help, but I am still learning and do not even know where to start ;-)

Thanks in advance,

Florian

[stebo85]

Dear @fphsFischmeister,

great to hear you are using neurodesk vnm :)

Adding the CONN toolbox should be quite straight forward, because they offer a standalone version (https://www.nitrc.org/frs/?group_id=279). Matlab toolboxes without a Matlab Runtime envrionment standalone version are on our todo list as well, but it will take a while to figure out how to manage the matlab licenses insides our containers :p

I give it a quick shot to add this and it would be great if you can test :)

Cheers
Steffen

[stebo85]

I tried getting the compiled version to work, but run into this error:
conn
Initializing MATLAB Runtime version 9.5
Loading MCR. Please wait...
PostVMInit failed to initialize com.mathworks.mwswing.MJStartupForDesktop
PostVMInit failed to initialize com.mathworks.mwswing.MJStartup

---

   Segmentation violation detected at Thu Jan 07 10:44:52 2021 +0000

---

Configuration:
Crash Decoding : Disabled - No sandbox or build area path
Crash Mode : continue (default)
Default Encoding : UTF-8
Deployed : true
GNU C Library : 2.27 stable
Graphics Driver : Unknown software
Java Version : Java 1.8.0_152-b16 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
MATLAB Architecture : glnxa64
MATLAB Entitlement ID : Unknown
MATLAB Root : /opt/matlabmcr-2018b/v95
MATLAB Version : 9.5.0.944444 (R2018b)
OpenGL : software
Operating System : Linux 4.14.35-1902.304.6.el7uek.x86_64 #2 SMP Thu Jul 2 18:16:54 PDT 2020 x86_64
Process ID : 178
Processor ID : x86 Family 6 Model 85 Stepping 4, GenuineIntel
Session Key : d7b8ba48-c6fb-44a1-900f-d3955540f272
Static TLS mitigation : Disabled: software OpenGL fallback
Window System : The X.Org Foundation (12008000), display :1.0

Fault Count: 1

Abnormal termination

Register State (from fault):
RAX = 0000000000000000 RBX = 00007efca4cf2f4c
RCX = 0000000000000000 RDX = 0000000000000028
RSP = 00007efca4cf2f20 RBP = 00007efca4cf2f80
RSI = 00007efc023dcad8 RDI = 00007efc9da65360

R8 = 0000000000000001 R9 = 00007efc9d9f4000
R10 = 0000000000000001 R11 = 00000000b0c26d7a
R12 = 00007efc023dcae1 R13 = 00007efc9da65360
R14 = 00007efc1a5fe8a0 R15 = 00007efc023dcae1

RIP = 00007efc9a3d0004 EFL = 0000000000010206

CS = 0033 FS = 0000 GS = 0000

Stack Trace (from fault):
[ 0] 0x00007efc9a3d0004 /opt/matlabmcr-2018b/v95/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+07208964
[ 1] 0x00007efc9a3d02ea /opt/matlabmcr-2018b/v95/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+07209706
[ 2] 0x00007efca280a841 bin/glnxa64/libmwjmi.so+00788545
[ 3] 0x00007efc0201a4c5 bin/glnxa64/libmwhg.so+02929861
[ 4] 0x00007efc020210cc bin/glnxa64/libmwhg.so+02957516
[ 5] 0x00007efc02024072 bin/glnxa64/libmwhg.so+02969714
[ 6] 0x00007efc0219da26 bin/glnxa64/libmwhg.so+04516390 _ZN7mwboost6detail8function17function_invoker0IPFN4mcos8COSValueEvES4_E6invokeERNS1_15function_bufferE+00000006
[ 7] 0x00007efc021a8811 bin/glnxa64/libmwhg.so+04560913 _ZN7hgutils22UserFcnDefaultProvider10getDefaultEv+00000033
[ 8] 0x00007efc01fe7c90 bin/glnxa64/libmwhg.so+02722960
[ 9] 0x00007efc02274f2a bin/glnxa64/libmwhg.so+05398314
[ 10] 0x00007efc02275895 bin/glnxa64/libmwhg.so+05400725
[ 11] 0x00007efc9b524a06 bin/glnxa64/libmwmcos_impl.so+02132486
[ 12] 0x00007efc9b69df61 bin/glnxa64/libmwmcos_impl.so+03678049
[ 13] 0x00007efc9b5eb8ce bin/glnxa64/libmwmcos_impl.so+02947278
[ 14] 0x00007efc9b5eba12 bin/glnxa64/libmwmcos_impl.so+02947602
[ 15] 0x00007efc9b6c6b93 bin/glnxa64/libmwmcos_impl.so+03845011
[ 16] 0x00007efc0201de83 bin/glnxa64/libmwhg.so+02944643
[ 17] 0x00007efc0201e8c0 bin/glnxa64/libmwhg.so+02947264
[ 18] 0x00007efc0201ec2e bin/glnxa64/libmwhg.so+02948142 _ZNSt17_Function_handlerIFN4mcos15COSInterfacePtrEvEPS2_E9_M_invokeERKSt9_Any_data+00000014
[ 19] 0x00007efc01a89241 bin/glnxa64/libmwhgutils.so+01077825 _ZN7hgutils12RootInstance15getRootInstanceENS0_13NullToleranceE+00000049
[ 20] 0x00007efc0201db2a bin/glnxa64/libmwhg.so+02943786
[ 21] 0x00007efc0217dc73 bin/glnxa64/libmwhg.so+04385907
[ 22] 0x00007efc0217e244 bin/glnxa64/libmwhg.so+04387396
[ 23] 0x00007efc02182d83 bin/glnxa64/libmwhg.so+04406659
[ 24] 0x00007efc02182f15 bin/glnxa64/libmwhg.so+04407061 MLInitialize_hg+00000261
[ 25] 0x00007efc0346d279 bin/glnxa64/libmwhgbuiltins.so+01856121 MLInitialize_hgbuiltins+00000025
[ 26] 0x00007efcb7bd078d bin/glnxa64/libmwm_dispatcher.so+00534413
[ 27] 0x00007efcb7bc23a2 bin/glnxa64/libmwm_dispatcher.so+00476066 _ZN18Mlm_MATLAB_fn_impl8try_loadEv+00000066
[ 28] 0x00007efcb7bc0375 bin/glnxa64/libmwm_dispatcher.so+00467829 _ZN18Mlm_MATLAB_fn_impl4loadEv+00000053
[ 29] 0x00007efcb7bb68c8 bin/glnxa64/libmwm_dispatcher.so+00428232 ZN18Mfh_MATLAB_fn_impl16dispatch_fh_implEMS_FviPP11mxArray_tagiS2_EiS2_iS2+00001032
[ 30] 0x00007efcb7bb6afe bin/glnxa64/libmwm_dispatcher.so+00428798 ZN18Mfh_MATLAB_fn_impl11dispatch_fhEiPP11mxArray_tagiS2+00000030
[ 31] 0x00007efcb5d58297 bin/glnxa64/libmwm_lxe.so+12862103
[ 32] 0x00007efcb5d58cff bin/glnxa64/libmwm_lxe.so+12864767
[ 33] 0x00007efcb5e5e219 bin/glnxa64/libmwm_lxe.so+13935129
[ 34] 0x00007efcb5de3861 bin/glnxa64/libmwm_lxe.so+13432929
[ 35] 0x00007efcb55c6b58 bin/glnxa64/libmwm_lxe.so+04926296
[ 36] 0x00007efcb55c933c bin/glnxa64/libmwm_lxe.so+04936508
[ 37] 0x00007efcb55c53cd bin/glnxa64/libmwm_lxe.so+04920269
[ 38] 0x00007efcb55bf0d1 bin/glnxa64/libmwm_lxe.so+04894929
[ 39] 0x00007efcb55bf309 bin/glnxa64/libmwm_lxe.so+04895497
[ 40] 0x00007efcb55c4bf6 bin/glnxa64/libmwm_lxe.so+04918262
[ 41] 0x00007efcb55c4cdf bin/glnxa64/libmwm_lxe.so+04918495
[ 42] 0x00007efcb56fd7e9 bin/glnxa64/libmwm_lxe.so+06199273
[ 43] 0x00007efcb5700f03 bin/glnxa64/libmwm_lxe.so+06213379
[ 44] 0x00007efcb5c27b31 bin/glnxa64/libmwm_lxe.so+11615025
[ 45] 0x00007efcb5bd66ec bin/glnxa64/libmwm_lxe.so+11282156
[ 46] 0x00007efcb5bdd818 bin/glnxa64/libmwm_lxe.so+11311128
[ 47] 0x00007efcb5bdf162 bin/glnxa64/libmwm_lxe.so+11317602
[ 48] 0x00007efcb5c7dd49 bin/glnxa64/libmwm_lxe.so+11967817
[ 49] 0x00007efcb5c7e2d1 bin/glnxa64/libmwm_lxe.so+11969233
[ 50] 0x00007efcb7bc7072 bin/glnxa64/libmwm_dispatcher.so+00495730
[ 51] 0x00007efcb7bb668d bin/glnxa64/libmwm_dispatcher.so+00427661 ZN18Mfh_MATLAB_fn_impl16dispatch_fh_implEMS_FviPP11mxArray_tagiS2_EiS2_iS2+00000461
[ 52] 0x00007efcb7bb6b2e bin/glnxa64/libmwm_dispatcher.so+00428846 ZN18Mfh_MATLAB_fn_impl22dispatch_fh_with_reuseEiPP11mxArray_tagiS2+00000030
[ 53] 0x00007efcb5e8858e bin/glnxa64/libmwm_lxe.so+14108046
[ 54] 0x00007efcb5bd53c6 bin/glnxa64/libmwm_lxe.so+11277254
[ 55] 0x00007efcb5c6be11 bin/glnxa64/libmwm_lxe.so+11894289
[ 56] 0x00007efcb5c6c641 bin/glnxa64/libmwm_lxe.so+11896385
[ 57] 0x00007efcbb4fb15e bin/glnxa64/libmwm_interpreter.so+00934238 inCallFcnWithTrap+00000078
[ 58] 0x00007efcbc95fcf1 bin/glnxa64/libmwmcr.so+00548081
[ 59] 0x00007efc9b5ea488 bin/glnxa64/libmwmcos_impl.so+02942088
[ 60] 0x00007efc9b5ed2ac bin/glnxa64/libmwmcos_impl.so+02953900
[ 61] 0x00007efc9b5f4952 bin/glnxa64/libmwmcos_impl.so+02984274
[ 62] 0x00007efc9b5e93b1 bin/glnxa64/libmwmcos_impl.so+02937777
[ 63] 0x00007efc9b691b0d bin/glnxa64/libmwmcos_impl.so+03627789
[ 64] 0x00007efcaf3b85ee bin/glnxa64/libmwlxeindexing.so+00873966
[ 65] 0x00007efcaf3ba930 bin/glnxa64/libmwlxeindexing.so+00882992
[ 66] 0x00007efcaf34f73f bin/glnxa64/libmwlxeindexing.so+00444223
[ 67] 0x00007efcaf35106c bin/glnxa64/libmwlxeindexing.so+00450668
[ 68] 0x00007efcaf3cb23a bin/glnxa64/libmwlxeindexing.so+00950842
[ 69] 0x00007efcaf36828d bin/glnxa64/libmwlxeindexing.so+00545421
[ 70] 0x00007efcaf3ae1d2 bin/glnxa64/libmwlxeindexing.so+00831954 ZN9MathWorks3lxe8at_rdot0EPvNS_2ts4TypeEPKvS1+00000146
[ 71] 0x00007efcb5df5a31 bin/glnxa64/libmwm_lxe.so+13507121
[ 72] 0x00007efcb55c6ced bin/glnxa64/libmwm_lxe.so+04926701
[ 73] 0x00007efcb55c933c bin/glnxa64/libmwm_lxe.so+04936508
[ 74] 0x00007efcb55c53cd bin/glnxa64/libmwm_lxe.so+04920269
[ 75] 0x00007efcb55bf0d1 bin/glnxa64/libmwm_lxe.so+04894929
[ 76] 0x00007efcb55bf309 bin/glnxa64/libmwm_lxe.so+04895497
[ 77] 0x00007efcb55c4bf6 bin/glnxa64/libmwm_lxe.so+04918262
[ 78] 0x00007efcb55c4cdf bin/glnxa64/libmwm_lxe.so+04918495
[ 79] 0x00007efcb56fd7e9 bin/glnxa64/libmwm_lxe.so+06199273
[ 80] 0x00007efcb5700f03 bin/glnxa64/libmwm_lxe.so+06213379
[ 81] 0x00007efcb5c27b31 bin/glnxa64/libmwm_lxe.so+11615025
[ 82] 0x00007efcb5d453a1 bin/glnxa64/libmwm_lxe.so+12784545
[ 83] 0x00007efcb5d4551d bin/glnxa64/libmwm_lxe.so+12784925
[ 84] 0x00007efcb7c3bbc8 bin/glnxa64/libmwm_dispatcher.so+00973768 ZN8Mfh_file16dispatch_fh_implEMS_FviPP11mxArray_tagiS2_EiS2_iS2+00001240
[ 85] 0x00007efcb7c3c02e bin/glnxa64/libmwm_dispatcher.so+00974894 ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2+00000030
[ 86] 0x00007efcb5d58297 bin/glnxa64/libmwm_lxe.so+12862103
[ 87] 0x00007efcb5d58cff bin/glnxa64/libmwm_lxe.so+12864767
[ 88] 0x00007efcb5e5e219 bin/glnxa64/libmwm_lxe.so+13935129
[ 89] 0x00007efcb5de3861 bin/glnxa64/libmwm_lxe.so+13432929
[ 90] 0x00007efcb55c6b58 bin/glnxa64/libmwm_lxe.so+04926296
[ 91] 0x00007efcb55c933c bin/glnxa64/libmwm_lxe.so+04936508
[ 92] 0x00007efcb55c53cd bin/glnxa64/libmwm_lxe.so+04920269
[ 93] 0x00007efcb55bf0d1 bin/glnxa64/libmwm_lxe.so+04894929
[ 94] 0x00007efcb55bf309 bin/glnxa64/libmwm_lxe.so+04895497
[ 95] 0x00007efcb55c4bf6 bin/glnxa64/libmwm_lxe.so+04918262
[ 96] 0x00007efcb55c4cdf bin/glnxa64/libmwm_lxe.so+04918495
[ 97] 0x00007efcb56fd7e9 bin/glnxa64/libmwm_lxe.so+06199273
[ 98] 0x00007efcb5700f03 bin/glnxa64/libmwm_lxe.so+06213379
[ 99] 0x00007efcb5c27b31 bin/glnxa64/libmwm_lxe.so+11615025
[100] 0x00007efcb5bd66ec bin/glnxa64/libmwm_lxe.so+11282156
[101] 0x00007efcb5bdd818 bin/glnxa64/libmwm_lxe.so+11311128
[102] 0x00007efcb5bdf162 bin/glnxa64/libmwm_lxe.so+11317602
[103] 0x00007efcb5c6da55 bin/glnxa64/libmwm_lxe.so+11901525
[104] 0x00007efcb5c6de0a bin/glnxa64/libmwm_lxe.so+11902474
[105] 0x00007efcbc9ab3ca bin/glnxa64/libmwmcr.so+00857034
[106] 0x00007efcbc979cd3 bin/glnxa64/libmwmcr.so+00654547 ZN14cmddistributor15PackagedTaskIIP10invokeFuncIN7mwboost8functionIFvvEEEEENS2_10shared_ptrINS2_13unique_futureIDTclfp_EEEEEERKT+00000067
[107] 0x00007efcbc979ec8 bin/glnxa64/libmwmcr.so+00655048 _ZNSt17_Function_handlerIFN7mwboost3anyEvEZN14cmddistributor15PackagedTaskIIP10createFuncINS0_8functionIFvvEEEEESt8functionIS2_ET_EUlvE_E9_M_invokeERKSt9_Any_data+00000024
[108] 0x00007efcba1eb08c bin/glnxa64/libmwiqm.so+00897164 _ZN7mwboost6detail8function21function_obj_invoker0ISt8functionIFNS_3anyEvEES4_E6invokeERNS1_15function_bufferE+00000028
[109] 0x00007efcba1ead45 bin/glnxa64/libmwiqm.so+00896325 _ZN3iqm18PackagedTaskPlugin7executeEP15inWorkSpace_tag+00000437
[110] 0x00007efcbc9a7075 bin/glnxa64/libmwmcr.so+00839797
[111] 0x00007efcba1c9517 bin/glnxa64/libmwiqm.so+00759063
[112] 0x00007efcba1ad6ba bin/glnxa64/libmwiqm.so+00644794
[113] 0x00007efcba1ae20f bin/glnxa64/libmwiqm.so+00647695
[114] 0x00007efcbc98734e bin/glnxa64/libmwmcr.so+00709454
[115] 0x00007efcbc987b08 bin/glnxa64/libmwmcr.so+00711432
[116] 0x00007efcbc97fd92 bin/glnxa64/libmwmcr.so+00679314
[117] 0x00007efcc4d006db /lib/x86_64-linux-gnu/libpthread.so.0+00030427
[118] 0x00007efcc6ea671f /lib/x86_64-linux-gnu/libc.so.6+01185567 clone+00000063
[119] 0x0000000000000000 +00000000

[fphsFischmeister]

Hi Steffen,
just pulled the latest vnm docker container, however, could not find the conn toolbox within the selection.
Best, Florian

[stebo85]

correct - it's not yet in there because it crashes when starting the conn toolbox standalone version - maybe it was compiled incorrectly and needs to be compiled again :?

[civier]

Hi Steffen,
You can try posting a question on the CONN discussion forum. Alfonso (CONN's developer) is very good in responding to questions promptly. If he doesn't get back to you soon, let me know, and I'll contact him privately (he his a former labmate and a friend of mine).
Welcome to the lockdown club :-(
Oren

[fphsFischmeister]

Just tried the new 20b version and run into the following error:

To run container outside of this environment: ml conn/18b
+++++++++++++++++++++ conn +++++++++++++++++++++++++

Singularity> conn
Initializing MATLAB Runtime version 9.9
Loading MCR. Please wait...
PostVMInit failed to initialize com.mathworks.mwswing.MJStartupForDesktop
PostVMInit failed to initialize com.mathworks.mwswing.MJStartup
Could not find java/awt/Component

Error in javaclasspath>local_javapath (line 137)

Error in javaclasspath (line 65)

Error in javaaddpath (line 69)

MATLAB:Java:GenericException

thanks again! Florian

[stebo85]

yes, this problem comes up when I try to compile the latest version in MCR 9.9 - I am not sure if this problem comes before the libc.so.6 issues or if I managed to get past this problem.

[stebo85]

@fphsFischmeister - I finally got it to work :) The java error was indeed the last problem and adding openjdk-8-jre did the trick :) I am just cleaning up the development mess and push a new version. I let you know when it's ready for testing.

[stebo85]

Dear @fphsFischmeister,

Conn 20b is now added to the latest VNM version :)

Can you give it a thorough test and let me know what works and what doesn't?
sudo docker run --privileged --name vnm -e RESOLUTION=1620x960 -e USER=neuro -v /mnt/FileSystem-20200817-0905-05/vnm-test:/vnm -v /dev/shm:/dev/shm -p 6080:80 -p 5900:5900 vnmd/vnm:20210109

[fphsFischmeister]

Dear Steffen,

a bit more testing revealed the following:

1. the /vnm directory is only mounted within the singularity container when loaded from the bash. Starting from the menu, the /vnm directory is empty. This also holds for itksnap and spm - only tested these.

2. editing the $bind_singularity variable within .bashrc I can add any externally to vnm mounted directory to singularity. However, still the above point 1 applies.

So when everything is mounted correctly, the conn-toolbox is working perfectly. Thus I would suggest to mark this done and I will open an issue related to the mounting problem.

best,

Florian

[stebo85]

Dear @fphsFischmeister,

Very interesting - It only appears when starting the GUI options of the tools. I have an idea what goes wrong there.

Thank you for finding this! I hope to have this fixed in a bit :)

Cheers
Steffen

[stebo85]

Dear @fphsFischmeister ,

I think I found an elegant solution for the problem :)
Could you test it?

sudo docker run --privileged --name vnm -e RESOLUTION=1620x960 -e USER=neuro -v ~/vnm:/vnm -v /dev/shm:/dev/shm -p 6080:80 -p 5900:5900 vnmd/vnm:20210130

Cheers
Steffen

[fphsFischmeister]

Thank you so much! Your solution is working like a charm.

However, I have one simple remark: To be scalable in the future, I would refrain from having 20+ directories in the https://github.com/NeuroDesk/caid/blob/master/recipes/globalMountPointList.txt and add them using a script. Instead, I would only add a small number of directories, each with a given purpose, like e.g.

• /data for all data directories,
• /media for external drives
• /autofs for automounts
• /scratch for scratch data
• /tmp for temp outside docker
  and ask users to add external directories accordingly using -v /xxx/mydata:/data/mydata.

Cheers, Florian

[stebo85]

Dear @fphsFischmeister,

Thank you for testing and great to hear it works :)

We haven't found a perfect solution for the mountpoints: A large part of our users run neurodesk directly on HPCs without the docker wrapper container - but most singularity installs on HPCs do not allow us to mount directories without these directories existing in the singularity image at build time. That's why we have the globalmountpoint file ... To keep it scalable and maintainable our CI automatically rebuilds all containers should anything be added to the globalmountpoint list. But of course this rebuild will get harder the more applications we have, so we need a better longterm solution. We are hoping for the new releases of singularity to be more widely installed on HPCs where mounting directories got a lot better :) and then we can hopefully move away from this interim solution.

Thank you for your input and thoughts
Cheers
Steffen