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emClarity_1_5_2_0: symbol lookup error #131

Closed Pengxin1028 closed 9 months ago

Pengxin1028 commented 3 years ago

Hi,

I am having issue of installing emClarity. I installed MATLABv99 but when I ran emClarity_1_5_2_0_v20b, I got the following message:

emClarity_1_5_2_0: symbol lookup error usr/local/MATLAB/MATLAB_Runtime/v99/sys/os/glnxa64/libstdc++.so.6: undefined symbol: __cxa_thread_atexit_impl

Can someone give me some suggestions? My system: Centos 7.

Best, Pengxin

bHimes commented 3 years ago

Please check the wiki ... you’ll need mcr. 2020b

Ben

On Mon, Feb 1, 2021 at 1:27 PM Pengxin1028 notifications@github.com wrote:

Hi,

I am having issue of installing emClarity. I installed MATLABv99 but when I ran emClarity_1_5_2_0_v20b, I got the following message:

emClarity_1_5_2_0: symbol lookup error usr/local/MATLAB/MATLAB_Runtime/v99/sys/os/glnxa64/libstdc++.so.6: undefined symbol: __cxa_thread_atexit_impl

Can someone give me some suggestions? My system: Centos 7.

Best, Pengxin

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Benjamin Himes

cryoEM methods development Grigorieff lab https://mail.hhmi.org/owa/redir.aspx?C=SbsCefkcbOt75jDyr05lpd3OifVN_utmfvnhZrtXS7Bl2i2eOXXVCA..&URL=http%3a%2f%2fgrigoriefflab.janelia.org%2f, HHMI Janelia Research Campus

cryoSTAC development @ emClarity https://mail.hhmi.org/owa/redir.aspx?C=8yDzXj54yTidMevTB7q5m3liEVwqAZ9LxuXQ4iYOVvtl2i2eOXXVCA..&URL=https%3a%2f%2fgithub.com%2fbHimes%2femClarity%2fwiki

Pengxin1028 commented 3 years ago

Hi Ben, Sorry to bother you. I do installed the "MATLAB_Runtime_R2020b_Update_3_glnxa64.zip" package as the wiki did.

cvsindelar commented 3 years ago

Hi all, I have a solution to this problem. It may be specific to CENTOS 7. Solution requires a full, working matlab installation. See the following link:

https://itectec.com/matlab/matlab-error-running-matlab-parallel-server-toolbox-admincenter/

You need to do the following before running emclarity: export LD_PRELOAD=[your matlabroot]/bin/glnxa64/glibc-2.17_shim.so"

cvsindelar commented 3 years ago

In case it helps, here is the glibc-2.17_shim.so library from our system:

glib_for_emc.zip

bHimes commented 3 years ago

Thanks Chuck!

Fwiw, starting vs 1.5.3.x i've fallen back to compiling on centos7, using Matlab 2019a, with cuda 10.0

In addition to the glibc compatibility issues, the newest matlab versions seem to produce very slow code.

We're still working out a couple of kinks (on 1.5.3.04) but overall, the beta version is pretty stable. Most people should wait for 1.5.3.1, but if you don't mind updating minor versions as we roll out small bug fixes, feel free to test.

Ben

On Wed, May 12, 2021 at 7:09 AM cvsindelar @.***> wrote:

Hi all, I have a solution to this problem. It may be specific to CENTOS 7. Solution requires a full, working matlab installation. See the following link:

https://itectec.com/matlab/matlab-error-running-matlab-parallel-server-toolbox-admincenter/

You need to do the following before running emclarity: export LD_PRELOAD="/bin/glnxa64/glibc-2.17_shim.so"

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/bHimes/emClarity/issues/131#issuecomment-839685277, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAXPLGE6FDPGM6MJTP63UPLTNJOWBANCNFSM4W5FNXYQ .

--

Benjamin Himes, PhD

cryoEM methods development HHMI, RNA Therapeutics Institute, University of Massachusetts Medical School

cryo-STA development @ emClarity https://github.com/bHimes/emClarity Visual Proteomics @ cisTEM https://github.com/timothygrant80/cisTEM

hongzhan2015 commented 3 years ago

Super thanks Ben and Chuck!

Hong

On Wed, May 12, 2021 at 7:40 AM B.A.Himes @.***> wrote:

Thanks Chuck!

Fwiw, starting vs 1.5.3.x i've fallen back to compiling on centos7, using Matlab 2019a, with cuda 10.0

In addition to the glibc compatibility issues, the newest matlab versions seem to produce very slow code.

We're still working out a couple of kinks (on 1.5.3.04) but overall, the beta version is pretty stable. Most people should wait for 1.5.3.1, but if you don't mind updating minor versions as we roll out small bug fixes, feel free to test.

Ben

On Wed, May 12, 2021 at 7:09 AM cvsindelar @.***> wrote:

Hi all, I have a solution to this problem. It may be specific to CENTOS 7. Solution requires a full, working matlab installation. See the following link:

https://itectec.com/matlab/matlab-error-running-matlab-parallel-server-toolbox-admincenter/

You need to do the following before running emclarity: export LD_PRELOAD="/bin/glnxa64/glibc-2.17_shim.so"

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/bHimes/emClarity/issues/131#issuecomment-839685277, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAXPLGE6FDPGM6MJTP63UPLTNJOWBANCNFSM4W5FNXYQ

.

--

Benjamin Himes, PhD

cryoEM methods development HHMI, RNA Therapeutics Institute, University of Massachusetts Medical School

cryo-STA development @ emClarity https://github.com/bHimes/emClarity Visual Proteomics @ cisTEM https://github.com/timothygrant80/cisTEM

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