Help needed in China, no access to google drive... #72
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Hi Gaoxing,
Do you have a Matlab license? I could write a brief guide on compiling from
the source code.
Otherwise, we can figure something else out.
Ben
…On Wed, Sep 5, 2018, 2:53 AM hgxy15 ***@***.***> wrote:
Hi, Ben, I just heard the talk on emClarity on Kuo Symposium, Fantastic
results! really eager to try this software on my data set, but I currently
have no access to google drive in china, is there any other way emClarity
is distributed? Many thanks in advance!
Gaoxing
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I do have a matlab license, I tried using the mCompile.sh emClarity.m to install the emClarity from source code, but when I type ./emClarity_gaoxing_1_0_0 in the bin directory, the program gives the following error: Error in emClarity (line 8) MATLAB:badsubscript Gaoxing |
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I'm currently using Matlab 2018a and the MCR I installed is also the 2018Ra version. The cuda version is cuda9.1. |
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Hi Gaoxing,
So I haven't tested yet on 2018 versions of matlab, and while it *should*
work based on what I remember reading on the release notes, I can only say
that it *will* work for release 2017b
Did you compile on your own using *mcc* or did you run the following in
your testScripts dir? I assume you did.
.../testScripts ] $ > ./mCompile emClarity
After emClarity is compiled, you can't call the binary directly, rather you
must use the shell script provided, which in this case is called
emClarity_17b. This script is also generated by the mCompile shell script
when you use it to compile the code.
Alternatively, you could try running emClarity from within an interactive
session in matlab. I provided some instructions on this sometime in the
last week, and you should be able to search for that message in the
emClarity google group archive.
Let me know if either of those solutions work, or if you need more specific
instructions on how to carry them out.
Best,
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 Wed, Sep 5, 2018 at 8:52 AM hgxy15 ***@***.***> wrote:
I'm currently using Matlab 2018a and the MCR I installed is also the
2018Ra version. The cuda version is cuda9.1.
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Hi, Ben, many thanks for the instruction! emClarity version fa82c80 Error using emClarity (line 40) Best, |
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Hi Gaoxing,
emClarity is really just a command line wrapper to my 3d gpu-accelerated
image processing library. It seems maybe you are hoping for a GUI to pop up
when you run "emClarity" ?
I would place a softlink in your local bin directory so that running
$ emClarity <command name>
actually calls your "emClarity_gaoxing_17b"
Then you could run
$ emClarity check
# verify your installation
$ emClarity help
# for a list of functions
$ emClarity <command name> <argument list>
# to carry out various operations as described in the documentation
(emClarity/docs)
HTH
Ben
…On Wed, Sep 5, 2018, 10:02 PM hgxy15 ***@***.***> wrote:
Hi, Ben, many thanks for the instruction!
Yes, I did run ./mCompile emClarity in the Testscripts directory and I
find the emClarity_17b (in this case called emClarity_gaoxing_17b) in the
bin directory.
However, when I run emClarity_gaoxing_17b, the program gives the following
error:
***************************************
emClarity version fa82c80
<fa82c80>
run starting on 06-Sep-2018 09:54:53
cmd
***************************************
Error using emClarity (line 40)
\n\n\tRun with help for a list of functions\n\n
Best,
Gaoxing
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Hi, Ben, |
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Hi Gaoxing,
The Matlab compile runtime (MCR) version is entirely dependent on the
version of Matlab used at compile time.
The only way to change the MCR required, is to compile it yourself from
source using a different Matlab version.
Ben
…On Thu, Sep 6, 2018, 8:05 AM hgxy15 ***@***.***> wrote:
Hi, Ben,
Thanks for the help ! I just managed to find a way to gain access to the
google drive and obtained the binary distribution, I think the binary is
looking for MCR9.3 which is for R2017b,so I'm know installing Matlab 2017b
on a different machine, I don't know if there's any way to change this or
is this specified during compilation ?
Best,
Gaoxing
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Hi Ben, Many thanks for the help! I now have emClarity running on a R2017b version of MATLAB with MCR 9.3. I 'm still going through the tutorial, will keep you updated if anything good comes up. Best, |
Hi, Ben, I just heard the talk on emClarity on Kuo Symposium, Fantastic results! really eager to try this software on my data set, but I currently have no access to google drive in china, is there any other way emClarity is distributed? Many thanks in advance!
Gaoxing
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