Undefined symbol: "_Z14standaloneMainRKST6vectorIssSaIssEEbb" during installation

[BuddySphinx]

I am trying to install emClarity on my local desktop via Matlab MCR. When I ran emClairy execution file, it raised such error. Could you help me understand what it is?

[bHimes]

Could you describe in some more detail what you did? I.e. What commands did you use to install:

1) the Matlab mcr 2) emClarity

And what command did you run to test?

(Exactly what you typed in the command line please)

Best

Ben

On Wed, Jan 23, 2019, 11:10 AM BuddySphinx <notifications@github.com wrote:

I am trying to install emClarity on my local desktop via Matlab MCR. When I ran emClairy execution file, it raised such error. Could you help me understand what it is?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/bHimes/emClarity/issues/91, or mute the thread https://github.com/notifications/unsubscribe-auth/AC71mIZudlrPoJctg4s0wIDPfTgPuHApks5vGIllgaJpZM4aPHJl .

[BuddySphinx]

Hi Ben, I downloaded matlab mcr from the matlab website for 2017b version. I unziped into the folder I created under emClarity folder, named "MCR" and I installed mcr exactly as suggested from the Wiki. Then I modified the emClarity_17b shell script with my path to the mcr_bash.sh file. Inside mcr_bash.sh I just added the $LD_LIBRARY_PATH variable by using "export LD_LIBRARY_PATH ="${LD_LIBRARY_PATH}:mypath" and ensure this will work, I also added it to my .bashrc file. Then I ran the emClarity execution file, it raised such error. Could you tell me what I did wrong? I tested both versions, the same issue. One thing I should mention is that Chimera is currently not installed on my desktop due to some unknown issue with tkiner module, but I could not see why it would affect the installation of emClarity? Best, Yangqi

bHimes notifications@github.com 于2019年1月23日周三 下午5:03写道：

Could you describe in some more detail what you did? I.e. What commands did you use to install:

1) the Matlab mcr 2) emClarity

And what command did you run to test?

(Exactly what you typed in the command line please)

Best

Ben

On Wed, Jan 23, 2019, 11:10 AM BuddySphinx <notifications@github.com wrote:

I am trying to install emClarity on my local desktop via Matlab MCR. When I ran emClairy execution file, it raised such error. Could you help me understand what it is?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/bHimes/emClarity/issues/91, or mute the thread < https://github.com/notifications/unsubscribe-auth/AC71mIZudlrPoJctg4s0wIDPfTgPuHApks5vGIllgaJpZM4aPHJl

.

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[bHimes]

Hi Yangqi,

Can you run the following and send the produced text file?

$ which emClarity >> logForBen.txt $ emClarity check >> logForBen.txt $ chimera >> logForBen.txt

thanks

On Wed, Jan 23, 2019, 6:29 PM BuddySphinx <notifications@github.com wrote:

Hi Ben, I downloaded matlab mcr from the matlab website for 2017b version. I unziped into the folder I created under emClarity folder, named "MCR" and I installed mcr exactly as suggested from the Wiki. Then I modified the emClarity_17b shell script with my path to the mcr_bash.sh file. Inside mcr_bash.sh I just added the $LD_LIBRARY_PATH variable by using "export LD_LIBRARY_PATH ="${LD_LIBRARY_PATH}:mypath" and ensure this will work, I also added it to my .bashrc file. Then I ran the emClarity execution file, it raised such error. Could you tell me what I did wrong? I tested both versions, the same issue. One thing I should mention is that Chimera is currently not installed on my desktop due to some unknown issue with tkiner module, but I could not see why it would affect the installation of emClarity? Best, Yangqi

bHimes notifications@github.com 于2019年1月23日周三 下午5:03写道：

Could you describe in some more detail what you did? I.e. What commands did you use to install:

1) the Matlab mcr 2) emClarity

And what command did you run to test?

(Exactly what you typed in the command line please)

Best

Ben

On Wed, Jan 23, 2019, 11:10 AM BuddySphinx <notifications@github.com wrote:

I am trying to install emClarity on my local desktop via Matlab MCR. When I ran emClairy execution file, it raised such error. Could you help me understand what it is?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/bHimes/emClarity/issues/91, or mute the thread <

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.

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[BuddySphinx]

Hi Ben, My emClarity was not installed properly, so the which command did not work on that. I don't have chimera installed either due to some unknown issue. Please see other information attached. Best, Yangqi

bHimes notifications@github.com 于2019年1月24日周四 上午7:23写道：

Hi Yangqi,

Can you run the following and send the produced text file?

$ which emClarity >> logForBen.txt $ emClarity check >> logForBen.txt $ chimera >> logForBen.txt

thanks

On Wed, Jan 23, 2019, 6:29 PM BuddySphinx <notifications@github.com wrote:

Hi Ben, I downloaded matlab mcr from the matlab website for 2017b version. I unziped into the folder I created under emClarity folder, named "MCR" and I installed mcr exactly as suggested from the Wiki. Then I modified the emClarity_17b shell script with my path to the mcr_bash.sh file. Inside mcr_bash.sh I just added the $LD_LIBRARY_PATH variable by using "export LD_LIBRARY_PATH ="${LD_LIBRARY_PATH}:mypath" and ensure this will work, I also added it to my .bashrc file. Then I ran the emClarity execution file, it raised such error. Could you tell me what I did wrong? I tested both versions, the same issue. One thing I should mention is that Chimera is currently not installed on my desktop due to some unknown issue with tkiner module, but I could not see why it would affect the installation of emClarity? Best, Yangqi

bHimes notifications@github.com 于2019年1月23日周三 下午5:03写道：

Could you describe in some more detail what you did? I.e. What commands did you use to install:

1) the Matlab mcr 2) emClarity

And what command did you run to test?

(Exactly what you typed in the command line please)

Best

Ben

On Wed, Jan 23, 2019, 11:10 AM BuddySphinx <notifications@github.com wrote:

I am trying to install emClarity on my local desktop via Matlab MCR. When I ran emClairy execution file, it raised such error. Could you help me understand what it is?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/bHimes/emClarity/issues/91, or mute the thread <

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.

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/usr/bin/which: no emClarity in (/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/install/IHRSR_v1.5:/home/install/spider/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/spuser/anaconda3/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/install/IHRSR_v1.5:/home/install/spider/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/install/smappoi:/home/install/spring_v0-86-1661/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/data/newspring/spring_v0-86-1661/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi:/home/install/spring_v0-86-1661/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/data/newspring/spring_v0-86-1661/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi) ./emClarity_1_0_0: symbol lookup error: ./emClarity_1_0_0: undefined symbol: _Z14standaloneMainRKSt6vectorISsSaISsEEbb

[bHimes]

Hi Yangqi,

So I guess your operating system does not know where to find emClarity then.

Any program that is installed must be on your system path, in order for the OS to find it. The "path" is the long error message printed to your terminal when you ran "which emClarity", and included at the end of the message. This can also be printed for inspection by running

$ echo ${PATH}

Wherever you put the script that runs emClarity ( it should be called emClarity_17b unless you renamed it) must be added to your path.

Say it was in "/home/install/emClarity/emClarity_17b"

You would need to add the following line to your ~/.bashrc

export PATH="/home/install/emClarity/emClarity_17b":${PATH}

I guess I should include some mention of this in the tutorial - does this fix your issue?

Ben

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

---

On Thu, Jan 24, 2019 at 3:50 PM BuddySphinx notifications@github.com wrote:

Hi Ben, My emClarity was not installed properly, so the which command did not work on that. I don't have chimera installed either due to some unknown issue. Please see other information attached. Best, Yangqi

bHimes notifications@github.com 于2019年1月24日周四 上午7:23写道：

Hi Yangqi,

Can you run the following and send the produced text file?

$ which emClarity >> logForBen.txt $ emClarity check >> logForBen.txt $ chimera >> logForBen.txt

thanks

On Wed, Jan 23, 2019, 6:29 PM BuddySphinx <notifications@github.com wrote:

Hi Ben, I downloaded matlab mcr from the matlab website for 2017b version. I unziped into the folder I created under emClarity folder, named "MCR" and I installed mcr exactly as suggested from the Wiki. Then I modified the emClarity_17b shell script with my path to the mcr_bash.sh file. Inside mcr_bash.sh I just added the $LD_LIBRARY_PATH variable by using "export LD_LIBRARY_PATH ="${LD_LIBRARY_PATH}:mypath" and ensure this will work, I also added it to my .bashrc file. Then I ran the emClarity execution file, it raised such error. Could you tell me what I did wrong? I tested both versions, the same issue. One thing I should mention is that Chimera is currently not installed on my desktop due to some unknown issue with tkiner module, but I could not see why it would affect the installation of emClarity? Best, Yangqi

bHimes notifications@github.com 于2019年1月23日周三 下午5:03写道：

Could you describe in some more detail what you did? I.e. What commands did you use to install:

1) the Matlab mcr 2) emClarity

And what command did you run to test?

(Exactly what you typed in the command line please)

Best

Ben

On Wed, Jan 23, 2019, 11:10 AM BuddySphinx <notifications@github.com wrote:

I am trying to install emClarity on my local desktop via Matlab MCR. When I ran emClairy execution file, it raised such error. Could you help me understand what it is?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/bHimes/emClarity/issues/91, or mute the thread <

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.

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.

/usr/bin/which: no emClarity in (/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/install/IHRSR_v1.5:/home/install/spider/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/spuser/anaconda3/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/install/IHRSR_v1.5:/home/install/spider/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/install/smappoi:/home/install/spring_v0-86-1661/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/data/newspring/spring_v0-86-1661/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi:/home/install/spring_v0-86-1661/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/data/newspring/spring_v0-86-1661/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi) ./emClarity_1_0_0: symbol lookup error: ./emClarity_1_0_0: undefined symbol: _Z14standaloneMainRKSt6vectorISsSaISsEEbb

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[BuddySphinx]

Hi Ben, I added to the PATH and I think I no longer get the issue with "unknown characters". But I seem to have some matlab license issue, I will troubleshoot a bit more and update if it works. Best, Yangqi

bHimes notifications@github.com 于2019年1月24日周四 下午4:53写道：

Hi Yangqi,

So I guess your operating system does not know where to find emClarity then.

Any program that is installed must be on your system path, in order for the OS to find it. The "path" is the long error message printed to your terminal when you ran "which emClarity", and included at the end of the message. This can also be printed for inspection by running

$ echo ${PATH}

Wherever you put the script that runs emClarity ( it should be called emClarity_17b unless you renamed it) must be added to your path.

Say it was in "/home/install/emClarity/emClarity_17b"

You would need to add the following line to your ~/.bashrc

export PATH="/home/install/emClarity/emClarity_17b":${PATH}

I guess I should include some mention of this in the tutorial - does this fix your issue?

Ben

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

---

On Thu, Jan 24, 2019 at 3:50 PM BuddySphinx notifications@github.com wrote:

Hi Ben, My emClarity was not installed properly, so the which command did not work on that. I don't have chimera installed either due to some unknown issue. Please see other information attached. Best, Yangqi

bHimes notifications@github.com 于2019年1月24日周四 上午7:23写道：

Hi Yangqi,

Can you run the following and send the produced text file?

$ which emClarity >> logForBen.txt $ emClarity check >> logForBen.txt $ chimera >> logForBen.txt

thanks

On Wed, Jan 23, 2019, 6:29 PM BuddySphinx <notifications@github.com wrote:

Hi Ben, I downloaded matlab mcr from the matlab website for 2017b version. I unziped into the folder I created under emClarity folder, named "MCR" and I installed mcr exactly as suggested from the Wiki. Then I modified the emClarity_17b shell script with my path to the mcr_bash.sh file. Inside mcr_bash.sh I just added the $LD_LIBRARY_PATH variable by using "export LD_LIBRARY_PATH ="${LD_LIBRARY_PATH}:mypath" and ensure this will work, I also added it to my .bashrc file. Then I ran the emClarity execution file, it raised such error. Could you tell me what I did wrong? I tested both versions, the same issue. One thing I should mention is that Chimera is currently not installed on my desktop due to some unknown issue with tkiner module, but I could not see why it would affect the installation of emClarity? Best, Yangqi

bHimes notifications@github.com 于2019年1月23日周三 下午5:03写道：

Could you describe in some more detail what you did? I.e. What commands did you use to install:

1) the Matlab mcr 2) emClarity

And what command did you run to test?

(Exactly what you typed in the command line please)

Best

Ben

On Wed, Jan 23, 2019, 11:10 AM BuddySphinx < notifications@github.com wrote:

I am trying to install emClarity on my local desktop via Matlab MCR. When I ran emClairy execution file, it raised such error. Could you help me understand what it is?

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.

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.

/usr/bin/which: no emClarity in

(/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/install/IHRSR_v1.5:/home/install/spider/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/spuser/anaconda3/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/install/IHRSR_v1.5:/home/install/spider/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/install/smappoi:/home/install/spring_v0-86-1661/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/data/newspring/spring_v0-86-1661/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi:/home/install/spring_v0-86-1661/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/data/newspring/spring_v0-86-1661/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi) ./emClarity_1_0_0: symbol lookup error: ./emClarity_1_0_0: undefined symbol: _Z14standaloneMainRKSt6vectorISsSaISsEEbb

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.

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[BuddySphinx]

Hi Ben, It's been a while and I finally figured out my matlab issue and I can lauch matlab. However, when I tried to run emClarity with ./emClarity_1_1_2 check it said MATLAB:badsubscript. It seems like the emClarity may have a different alias for matlab? Since I lauched matlab with just matlab instead of uppercase. Could you help me understand how to fix that? Best, Yangqi

bHimes notifications@github.com 于2019年1月24日周四 下午4:53写道：

Hi Yangqi,

So I guess your operating system does not know where to find emClarity then.

Any program that is installed must be on your system path, in order for the OS to find it. The "path" is the long error message printed to your terminal when you ran "which emClarity", and included at the end of the message. This can also be printed for inspection by running

$ echo ${PATH}

Wherever you put the script that runs emClarity ( it should be called emClarity_17b unless you renamed it) must be added to your path.

Say it was in "/home/install/emClarity/emClarity_17b"

You would need to add the following line to your ~/.bashrc

export PATH="/home/install/emClarity/emClarity_17b":${PATH}

I guess I should include some mention of this in the tutorial - does this fix your issue?

Ben

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

---

On Thu, Jan 24, 2019 at 3:50 PM BuddySphinx notifications@github.com wrote:

Hi Ben, My emClarity was not installed properly, so the which command did not work on that. I don't have chimera installed either due to some unknown issue. Please see other information attached. Best, Yangqi

bHimes notifications@github.com 于2019年1月24日周四 上午7:23写道：

Hi Yangqi,

Can you run the following and send the produced text file?

$ which emClarity >> logForBen.txt $ emClarity check >> logForBen.txt $ chimera >> logForBen.txt

thanks

On Wed, Jan 23, 2019, 6:29 PM BuddySphinx <notifications@github.com wrote:

Hi Ben, I downloaded matlab mcr from the matlab website for 2017b version. I unziped into the folder I created under emClarity folder, named "MCR" and I installed mcr exactly as suggested from the Wiki. Then I modified the emClarity_17b shell script with my path to the mcr_bash.sh file. Inside mcr_bash.sh I just added the $LD_LIBRARY_PATH variable by using "export LD_LIBRARY_PATH ="${LD_LIBRARY_PATH}:mypath" and ensure this will work, I also added it to my .bashrc file. Then I ran the emClarity execution file, it raised such error. Could you tell me what I did wrong? I tested both versions, the same issue. One thing I should mention is that Chimera is currently not installed on my desktop due to some unknown issue with tkiner module, but I could not see why it would affect the installation of emClarity? Best, Yangqi

bHimes notifications@github.com 于2019年1月23日周三 下午5:03写道：

Could you describe in some more detail what you did? I.e. What commands did you use to install:

1) the Matlab mcr 2) emClarity

And what command did you run to test?

(Exactly what you typed in the command line please)

Best

Ben

On Wed, Jan 23, 2019, 11:10 AM BuddySphinx < notifications@github.com wrote:

I am trying to install emClarity on my local desktop via Matlab MCR. When I ran emClairy execution file, it raised such error. Could you help me understand what it is?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/bHimes/emClarity/issues/91, or mute the thread <

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.

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.

/usr/bin/which: no emClarity in

(/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/install/IHRSR_v1.5:/home/install/spider/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/spuser/anaconda3/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/install/IHRSR_v1.5:/home/install/spider/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/install/smappoi:/home/install/spring_v0-86-1661/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/data/newspring/spring_v0-86-1661/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi:/home/install/spring_v0-86-1661/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/data/newspring/spring_v0-86-1661/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi) ./emClarity_1_0_0: symbol lookup error: ./emClarity_1_0_0: undefined symbol: _Z14standaloneMainRKSt6vectorISsSaISsEEbb

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.

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[bHimes]

Hi Yanqi,

You should not need to launch matlab to run emClarity.

Also, you do not run the emClarity binary (emClarity_1_1_2) directly. You run the script (emClarity_17b) which sets up the appropriate environment (points the binary to libraries in either your Matlab installation if you have one, or alternatively to your Matlab Compiler Runtime (MCR))

So you would run

./emClarity_17b check

(Or as I had previously suggested, make a link to this script somewhere like /usr/local/bin)

I'm sorry your having so much trouble with this. Is there someone in your group who might be able to help you out? This should be pretty straightforward.

Ben

---

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

---

---------- Forwarded message --------- From: BuddySphinx notifications@github.com Date: Mon, Feb 25, 2019 at 5:38 PM Subject: Re: [bHimes/emClarity] Undefined symbol: "_Z14standaloneMainRKST6vectorIssSaIssEEbb" during installation (#91) To: bHimes/emClarity emClarity@noreply.github.com Cc: bHimes himes.benjamin@gmail.com, Comment comment@noreply.github.com

Hi Ben, It's been a while and I finally figured out my matlab issue and I can lauch matlab. However, when I tried to run emClarity with ./emClarity_1_1_2 check it said MATLAB:badsubscript. It seems like the emClarity may have a different alias for matlab? Since I lauched matlab with just matlab instead of uppercase. Could you help me understand how to fix that? Best, Yangqi

bHimes notifications@github.com 于2019年1月24日周四 下午4:53写道：

Hi Yangqi,

So I guess your operating system does not know where to find emClarity then.

Any program that is installed must be on your system path, in order for the OS to find it. The "path" is the long error message printed to your terminal when you ran "which emClarity", and included at the end of the message. This can also be printed for inspection by running

$ echo ${PATH}

Wherever you put the script that runs emClarity ( it should be called emClarity_17b unless you renamed it) must be added to your path.

Say it was in "/home/install/emClarity/emClarity_17b"

You would need to add the following line to your ~/.bashrc

export PATH="/home/install/emClarity/emClarity_17b":${PATH}

I guess I should include some mention of this in the tutorial - does this fix your issue?

Ben

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

---

On Thu, Jan 24, 2019 at 3:50 PM BuddySphinx notifications@github.com wrote:

Hi Ben, My emClarity was not installed properly, so the which command did not work on that. I don't have chimera installed either due to some unknown issue. Please see other information attached. Best, Yangqi

bHimes notifications@github.com 于2019年1月24日周四 上午7:23写道：

Hi Yangqi,

Can you run the following and send the produced text file?

$ which emClarity >> logForBen.txt $ emClarity check >> logForBen.txt $ chimera >> logForBen.txt

thanks

On Wed, Jan 23, 2019, 6:29 PM BuddySphinx <notifications@github.com wrote:

Hi Ben, I downloaded matlab mcr from the matlab website for 2017b version. I unziped into the folder I created under emClarity folder, named "MCR" and I installed mcr exactly as suggested from the Wiki. Then I modified the emClarity_17b shell script with my path to the mcr_bash.sh file. Inside mcr_bash.sh I just added the $LD_LIBRARY_PATH variable by using "export LD_LIBRARY_PATH ="${LD_LIBRARY_PATH}:mypath" and ensure this will work, I also added it to my .bashrc file. Then I ran the emClarity execution file, it raised such error. Could you tell me what I did wrong? I tested both versions, the same issue. One thing I should mention is that Chimera is currently not installed on my desktop due to some unknown issue with tkiner module, but I could not see why it would affect the installation of emClarity? Best, Yangqi

bHimes notifications@github.com 于2019年1月23日周三 下午5:03写道：

Could you describe in some more detail what you did? I.e. What commands did you use to install:

1) the Matlab mcr 2) emClarity

And what command did you run to test?

(Exactly what you typed in the command line please)

Best

Ben

On Wed, Jan 23, 2019, 11:10 AM BuddySphinx < notifications@github.com wrote:

I am trying to install emClarity on my local desktop via Matlab MCR. When I ran emClairy execution file, it raised such error. Could you help me understand what it is?

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/usr/bin/which: no emClarity in

(/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/install/IHRSR_v1.5:/home/install/spider/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/spuser/anaconda3/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/install/IHRSR_v1.5:/home/install/spider/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/install/smappoi:/home/install/spring_v0-86-1661/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/data/newspring/spring_v0-86-1661/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi:/home/install/spring_v0-86-1661/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/data/newspring/spring_v0-86-1661/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi)

./emClarity_1_0_0: symbol lookup error: ./emClarity_1_0_0: undefined symbol: _Z14standaloneMainRKSt6vectorISsSaISsEEbb

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[BuddySphinx]

Hi Ben, Unfortunately, I am learning on my own, since I am the only one doing cryo in the lab. I managed to get it running and when I did emClarity_17b check, it output all the information correctly. However, when I tried to follow the tutorial by doing ctf estimate, using the command emClarity_17b ctf estimate template.m tilt 1, I got the following error: ignoring fixedStacks/tilt.fixed, because the file is not found (I did not do x-ray remove). Undefined function or variable 'pathName'.

Error in BH_ctf_Estimate (line 270)

Error in emClarity (line 339)

MATLAB:UndefinedFunction It seems that the Matlab installation folder is not properly setup? Should I just add matlab installation path to the Also, I have another question, which is can emClarity take input from user defined folder instead of "fixedStacks" and also if I have more than one gpu, how can I specify in the command line. I already added nGPUs=2 in the parameter file, but when I tried running the command line, it still sent all the job to one gpu. I am sorry to bother you with all these questions. Best, Yangqi

bHimes notifications@github.com 于2019年2月25日周一 下午6:29写道：

Hi Yanqi,

You should not need to launch matlab to run emClarity.

Also, you do not run the emClarity binary (emClarity_1_1_2) directly. You run the script (emClarity_17b) which sets up the appropriate environment (points the binary to libraries in either your Matlab installation if you have one, or alternatively to your Matlab Compiler Runtime (MCR))

So you would run

./emClarity_17b check

(Or as I had previously suggested, make a link to this script somewhere like /usr/local/bin)

I'm sorry your having so much trouble with this. Is there someone in your group who might be able to help you out? This should be pretty straightforward.

Ben

---

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

---

---------- Forwarded message --------- From: BuddySphinx notifications@github.com Date: Mon, Feb 25, 2019 at 5:38 PM Subject: Re: [bHimes/emClarity] Undefined symbol: "_Z14standaloneMainRKST6vectorIssSaIssEEbb" during installation (#91) To: bHimes/emClarity emClarity@noreply.github.com Cc: bHimes himes.benjamin@gmail.com, Comment <comment@noreply.github.com

Hi Ben, It's been a while and I finally figured out my matlab issue and I can lauch matlab. However, when I tried to run emClarity with ./emClarity_1_1_2 check it said MATLAB:badsubscript. It seems like the emClarity may have a different alias for matlab? Since I lauched matlab with just matlab instead of uppercase. Could you help me understand how to fix that? Best, Yangqi

bHimes notifications@github.com 于2019年1月24日周四 下午4:53写道：

Hi Yangqi,

So I guess your operating system does not know where to find emClarity then.

Any program that is installed must be on your system path, in order for the OS to find it. The "path" is the long error message printed to your terminal when you ran "which emClarity", and included at the end of the message. This can also be printed for inspection by running

$ echo ${PATH}

Wherever you put the script that runs emClarity ( it should be called emClarity_17b unless you renamed it) must be added to your path.

Say it was in "/home/install/emClarity/emClarity_17b"

You would need to add the following line to your ~/.bashrc

export PATH="/home/install/emClarity/emClarity_17b":${PATH}

I guess I should include some mention of this in the tutorial - does this fix your issue?

Ben

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

---

On Thu, Jan 24, 2019 at 3:50 PM BuddySphinx notifications@github.com wrote:

Hi Ben, My emClarity was not installed properly, so the which command did not work on that. I don't have chimera installed either due to some unknown issue. Please see other information attached. Best, Yangqi

bHimes notifications@github.com 于2019年1月24日周四 上午7:23写道：

Hi Yangqi,

Can you run the following and send the produced text file?

$ which emClarity >> logForBen.txt $ emClarity check >> logForBen.txt $ chimera >> logForBen.txt

thanks

On Wed, Jan 23, 2019, 6:29 PM BuddySphinx <notifications@github.com wrote:

Hi Ben, I downloaded matlab mcr from the matlab website for 2017b version. I unziped into the folder I created under emClarity folder, named "MCR" and I installed mcr exactly as suggested from the Wiki. Then I modified the emClarity_17b shell script with my path to the mcr_bash.sh file. Inside mcr_bash.sh I just added the $LD_LIBRARY_PATH variable by using "export LD_LIBRARY_PATH ="${LD_LIBRARY_PATH}:mypath" and ensure this will work, I also added it to my .bashrc file. Then I ran the emClarity execution file, it raised such error. Could you tell me what I did wrong? I tested both versions, the same issue. One thing I should mention is that Chimera is currently not installed on my desktop due to some unknown issue with tkiner module, but I could not see why it would affect the installation of emClarity? Best, Yangqi

bHimes notifications@github.com 于2019年1月23日周三 下午5:03写道：

Could you describe in some more detail what you did? I.e. What commands did you use to install:

1) the Matlab mcr 2) emClarity

And what command did you run to test?

(Exactly what you typed in the command line please)

Best

Ben

On Wed, Jan 23, 2019, 11:10 AM BuddySphinx < notifications@github.com wrote:

I am trying to install emClarity on my local desktop via Matlab MCR. When I ran emClairy execution file, it raised such error. Could you help me understand what it is?

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/usr/bin/which: no emClarity in

(/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/install/IHRSR_v1.5:/home/install/spider/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/spuser/anaconda3/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/install/IHRSR_v1.5:/home/install/spider/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/install/smappoi:/home/install/spring_v0-86-1661/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/data/newspring/spring_v0-86-1661/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi:/home/install/spring_v0-86-1661/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/data/newspring/spring_v0-86-1661/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi)

./emClarity_1_0_0: symbol lookup error: ./emClarity_1_0_0: undefined symbol: _Z14standaloneMainRKSt6vectorISsSaISsEEbb

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[bHimes]

No worries, would you mind signing up for the Google groups mailing list, and reposting this and future questions there?

There is a link on the main page of the wiki.

Thank you

On Mon, Feb 25, 2019, 7:57 PM BuddySphinx notifications@github.com wrote:

Hi Ben, Unfortunately, I am learning on my own, since I am the only one doing cryo in the lab. I managed to get it running and when I did emClarity_17b check, it output all the information correctly. However, when I tried to follow the tutorial by doing ctf estimate, using the command emClarity_17b ctf estimate template.m tilt 1, I got the following error: ignoring fixedStacks/tilt.fixed, because the file is not found (I did not do x-ray remove). Undefined function or variable 'pathName'.

Error in BH_ctf_Estimate (line 270)

Error in emClarity (line 339)

MATLAB:UndefinedFunction It seems that the Matlab installation folder is not properly setup? Should I just add matlab installation path to the Also, I have another question, which is can emClarity take input from user defined folder instead of "fixedStacks" and also if I have more than one gpu, how can I specify in the command line. I already added nGPUs=2 in the parameter file, but when I tried running the command line, it still sent all the job to one gpu. I am sorry to bother you with all these questions. Best, Yangqi

bHimes notifications@github.com 于2019年2月25日周一 下午6:29写道：

Hi Yanqi,

You should not need to launch matlab to run emClarity.

Also, you do not run the emClarity binary (emClarity_1_1_2) directly. You run the script (emClarity_17b) which sets up the appropriate environment (points the binary to libraries in either your Matlab installation if you have one, or alternatively to your Matlab Compiler Runtime (MCR))

So you would run

./emClarity_17b check

(Or as I had previously suggested, make a link to this script somewhere like /usr/local/bin)

I'm sorry your having so much trouble with this. Is there someone in your group who might be able to help you out? This should be pretty straightforward.

Ben

---

Benjamin Himes

cryoEM methods development Grigorieff lab <

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, HHMI Janelia Research Campus

cryoSTAC development @emClarity <

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---

---------- Forwarded message --------- From: BuddySphinx notifications@github.com Date: Mon, Feb 25, 2019 at 5:38 PM Subject: Re: [bHimes/emClarity] Undefined symbol: "_Z14standaloneMainRKST6vectorIssSaIssEEbb" during installation (#91) To: bHimes/emClarity emClarity@noreply.github.com Cc: bHimes himes.benjamin@gmail.com, Comment < comment@noreply.github.com

Hi Ben, It's been a while and I finally figured out my matlab issue and I can lauch matlab. However, when I tried to run emClarity with ./emClarity_1_1_2 check it said MATLAB:badsubscript. It seems like the emClarity may have a different alias for matlab? Since I lauched matlab with just matlab instead of uppercase. Could you help me understand how to fix that? Best, Yangqi

bHimes notifications@github.com 于2019年1月24日周四 下午4:53写道：

Hi Yangqi,

So I guess your operating system does not know where to find emClarity then.

Any program that is installed must be on your system path, in order for the OS to find it. The "path" is the long error message printed to your terminal when you ran "which emClarity", and included at the end of the message. This can also be printed for inspection by running

$ echo ${PATH}

Wherever you put the script that runs emClarity ( it should be called emClarity_17b unless you renamed it) must be added to your path.

Say it was in "/home/install/emClarity/emClarity_17b"

You would need to add the following line to your ~/.bashrc

export PATH="/home/install/emClarity/emClarity_17b":${PATH}

I guess I should include some mention of this in the tutorial - does this fix your issue?

Ben

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

---

On Thu, Jan 24, 2019 at 3:50 PM BuddySphinx notifications@github.com wrote:

Hi Ben, My emClarity was not installed properly, so the which command did not work on that. I don't have chimera installed either due to some unknown issue. Please see other information attached. Best, Yangqi

bHimes notifications@github.com 于2019年1月24日周四 上午7:23写道：

Hi Yangqi,

Can you run the following and send the produced text file?

$ which emClarity >> logForBen.txt $ emClarity check >> logForBen.txt $ chimera >> logForBen.txt

thanks

On Wed, Jan 23, 2019, 6:29 PM BuddySphinx < notifications@github.com wrote:

Hi Ben, I downloaded matlab mcr from the matlab website for 2017b version. I unziped into the folder I created under emClarity folder, named "MCR" and I installed mcr exactly as suggested from the Wiki. Then I modified the emClarity_17b shell script with my path to the mcr_bash.sh file. Inside mcr_bash.sh I just added the $LD_LIBRARY_PATH variable by using "export LD_LIBRARY_PATH ="${LD_LIBRARY_PATH}:mypath" and ensure this will work, I also added it to my .bashrc file. Then I ran the emClarity execution file, it raised such error. Could you tell me what I did wrong? I tested both versions, the same issue. One thing I should mention is that Chimera is currently not installed on my desktop due to some unknown issue with tkiner module, but I could not see why it would affect the installation of emClarity? Best, Yangqi

bHimes notifications@github.com 于2019年1月23日周三 下午5:03写道：

Could you describe in some more detail what you did? I.e. What commands did you use to install:

1) the Matlab mcr 2) emClarity

And what command did you run to test?

(Exactly what you typed in the command line please)

Best

Ben

On Wed, Jan 23, 2019, 11:10 AM BuddySphinx < notifications@github.com wrote:

I am trying to install emClarity on my local desktop via Matlab MCR. When I ran emClairy execution file, it raised such error. Could you help me understand what it is?

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/usr/bin/which: no emClarity in

(/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/install/IHRSR_v1.5:/home/install/spider/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/spuser/anaconda3/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/home/install/IHRSR_v1.5:/home/install/spider/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/install/smappoi:/home/install/spring_v0-86-1661/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/data/newspring/spring_v0-86-1661/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi:/home/install/spring_v0-86-1661/bin:/home/install/arp_warp_7.6/bin/bin-x86_64-Linux:/home/install/ccp4-7.0/etc:/home/install/ccp4-7.0/bin:/data/newspring/spring_v0-86-1661/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/lib64/openmpi/bin/:/home/spuser/EMAN2/bin:/home/spuser/miniconda2/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/ssd/cryosparc_install/bin:/ssd/cryosparc_install/bin:/usr/lib64/openmpi/bin:/opt/motioncorr_v2.1/bin:/opt/frealign_v9.11/bin:/opt/EMAN2/bin:/opt/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/opt/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/spuser/.local/bin:/home/spuser/bin:/home/install/smappoi)

./emClarity_1_0_0: symbol lookup error: ./emClarity_1_0_0: undefined symbol: _Z14standaloneMainRKSt6vectorISsSaISsEEbb

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