Undefined symbol: "_Z14standaloneMainRKST6vectorIssSaIssEEbb" during installation #91
Comments
|
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 ***@***.*** 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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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 ***@***.***
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
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> .
>
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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 ***@***.*** 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 ***@***.***> 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 ***@***.***
> 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
> > <#91>, or mute the thread
> > <
>
https://github.com/notifications/unsubscribe-auth/AC71mIZudlrPoJctg4s0wIDPfTgPuHApks5vGIllgaJpZM4aPHJl
> >
> > .
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <#91 (comment)>,
> or mute the thread
> <
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>
> .
>
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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 ***@***.*** 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 ***@***.***> 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 ***@***.***
> > 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
> > > <#91>, or mute the thread
> > > <
> >
>
https://github.com/notifications/unsubscribe-auth/AC71mIZudlrPoJctg4s0wIDPfTgPuHApks5vGIllgaJpZM4aPHJl
> > >
> > > .
> > >
> >
> > —
> > You are receiving this because you authored the thread.
> > Reply to this email directly, view it on GitHub
> > <#91 (comment)
>,
> > or mute the thread
> > <
>
https://github.com/notifications/unsubscribe-auth/AQJ70xxYfsy2xyGAfP7HI7sE5tXeLe3Sks5vGNxHgaJpZM4aPHJl
> >
> > .
> >
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <#91 (comment)>,
> 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
|
|
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 ***@***.***> 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 ***@***.***
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 ***@***.***> 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 ***@***.***
> > > 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
> > > > <#91>, or mute the
thread
> > > > <
> > >
> >
>
https://github.com/notifications/unsubscribe-auth/AC71mIZudlrPoJctg4s0wIDPfTgPuHApks5vGIllgaJpZM4aPHJl
> > > >
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you authored the thread.
> > > Reply to this email directly, view it on GitHub
> > > <
#91 (comment)
> >,
> > > or mute the thread
> > > <
> >
>
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> > >
> > > .
> > >
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub
> > <#91 (comment)
>,
> > or mute the thread
> > <
>
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> >
> > .
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <#91 (comment)>,
> or mute the thread
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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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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 ***@***.***>
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 ***@***.***> 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 ***@***.***
> 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 ***@***.***> 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 <
***@***.***
> > > > 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
> > > > > <#91>, or mute the
> thread
> > > > > <
> > > >
> > >
> >
>
https://github.com/notifications/unsubscribe-auth/AC71mIZudlrPoJctg4s0wIDPfTgPuHApks5vGIllgaJpZM4aPHJl
> > > > >
> > > > > .
> > > > >
> > > >
> > > > —
> > > > You are receiving this because you authored the thread.
> > > > Reply to this email directly, view it on GitHub
> > > > <
> #91 (comment)
> > >,
> > > > or mute the thread
> > > > <
> > >
> >
>
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> > > >
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you commented.
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> > > <
#91 (comment)
> >,
> > > or mute the thread
> > > <
> >
>
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> > >
> > > .
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> >
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> > You are receiving this because you authored the thread.
> > Reply to this email directly, view it on GitHub
> > <#91 (comment)
>,
> > or mute the thread
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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
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <#91 (comment)>,
> or mute the thread
> <
https://github.com/notifications/unsubscribe-auth/AC71mJy6MpnZkMglGCoVOgPXkSdXf9MXks5vGhyGgaJpZM4aPHJl
>
> .
>
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Reply to this email directly, view it on GitHub
<#91 (comment)>,
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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 ***@***.***>
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 ***@***.***> 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 ***@***.***
> 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 ***@***.***> 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 <
***@***.***
> > > > 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
> > > > > <#91>, or mute the
> thread
> > > > > <
> > > >
> > >
> >
>
https://github.com/notifications/unsubscribe-auth/AC71mIZudlrPoJctg4s0wIDPfTgPuHApks5vGIllgaJpZM4aPHJl
> > > > >
> > > > > .
> > > > >
> > > >
> > > > —
> > > > You are receiving this because you authored the thread.
> > > > Reply to this email directly, view it on GitHub
> > > > <
> #91 (comment)
> > >,
> > > > or mute the thread
> > > > <
> > >
> >
>
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> > > >
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub
> > > <
#91 (comment)
> >,
> > > 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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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
<
>,
HHMI Janelia Research Campus
cryoSTAC development @emClarity
<
>
-------------------------
On Thu, Jan 24, 2019 at 3:50 PM BuddySphinx ***@***.***>
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 ***@***.***> 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 ***@***.***
> 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 ***@***.***> 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 <
***@***.***
> > > > 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
> > > > > <#91>, or mute the
> thread
> > > > > <
> > > >
> > >
> >
>
> > > > >
> > > > > .
> > > > >
> > > >
> > > > —
> > > > You are receiving this because you authored the thread.
> > > > Reply to this email directly, view it on GitHub
> > > > <
> #91 (comment)
> > >,
> > > > or mute the thread
> > > > <
> > >
> >
>
> > > >
> > > > .
> > > >
> > >
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#91 (comment)
> >,
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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
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <#91 (comment)>,
> or mute the thread
> <
>
> .
>
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#91 (comment)>,
or mute the thread
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.
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.
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|
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 ***@***.***>
Date: Mon, Feb 25, 2019 at 5:38 PM
Subject: Re: [bHimes/emClarity] Undefined symbol:
"_Z14standaloneMainRKST6vectorIssSaIssEEbb" during installation (#91)
To: bHimes/emClarity ***@***.***>
Cc: bHimes ***@***.***>, Comment ***@***.***
>
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 ***@***.***> 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 ***@***.***>
> 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 ***@***.***> 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 ***@***.***
> > 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 ***@***.***> 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 <
> ***@***.***
> > > > > 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
> > > > > > <#91>, or mute the
> > thread
> > > > > > <
> > > > >
> > > >
> > >
> >
>
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> > > > > >
> > > > > > .
> > > > > >
> > > > >
> > > > > —
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> > > > > <
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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
> >
> > —
> > You are receiving this because you commented.
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> > or mute the thread
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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 ***@***.***> 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 ***@***.***> 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 ***@***.***>
> Date: Mon, Feb 25, 2019 at 5:38 PM
> Subject: Re: [bHimes/emClarity] Undefined symbol:
> "_Z14standaloneMainRKST6vectorIssSaIssEEbb" during installation (#91)
> To: bHimes/emClarity ***@***.***>
> Cc: bHimes ***@***.***>, Comment <
***@***.***
> >
>
>
> 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 ***@***.***> 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 ***@***.***>
> > 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 ***@***.***> 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 <
***@***.***
> > > 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 ***@***.***> 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 <
> > ***@***.***
> > > > > > 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
> > > > > > > <#91>, or mute the
> > > thread
> > > > > > > <
> > > > > >
> > > > >
> > > >
> > >
> >
>
>
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> > > > > > >
> > > > > > > .
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> > > > > >
> > > > > > —
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> > > #91 (comment)
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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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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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