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StochasticAnalytics / emClarity

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Installing in centos #133

Closed whynotcat closed 3 years ago

whynotcat commented 3 years ago

Dear bHimes, I am a beginner in cryo-tomography and matlab, morever emClarity, I got a trouble in installing of emClarity, like this

(base) [root@lsb bin]# sh emClarity_1_5_0_2_v19a Found tmpfs /dev/shm with max mem 131914048 bytes using this for MCR_CACHE_ROOT

##############

    Created a tmp MCR_CACHE locally at /dev/shm/emC_tmp_28475
    Available mem is 125.803 GB
    Started emC_memClean to make sure it removed in the event of a crash.
    Default kill time is a max of 10080 minutes

##############

Index exceeds the number of array elements (1).

Error in emClarity (line 39)

MATLAB:badsubscript

I tried to install emClarity like this,

[shp@lsb bin]# vi emClarity_1_5_0_2_v19a

!/bin/bash

When this script is invoked, record the PID so that the EMC_tmpDir is deleted

even in the event of a crash. (With program script added from EMC_tmpDir.sh)

thisPID=$$

Please modify this line to point to the text file in your MCR root

where you pasted the lines suggested to add to LD_LIBRARY_PATH during install.

MCR_BASH="/work/thirdParty/MATLAB/mcr_bash.sh"

MCR_BASH=/usr/local/matlab_2019a/v96/mcr_bash.sh

Please modify this line to point to the install for emClarity binary

emClarity_ROOT=/work/emClarity

emClarity_ROOT=/home/shp/emclarity_1.5.0.2/bin

This is added in the middle of the emClarity run script. It does the following.

1 - check for temporary file systems so that some disk i/o can instead be kept in memory.

2 - minimally the MCR_CACHE_ROOT is set there (formerly .mcrCarch_9.3 which is default)

This avoids the problem where parallel pools are dying due to either slow filesystems

or conflicts with other parpools from competing nodes.

3 - Fall back to $TMPDIR or /tmp if no tmpfs is found.

4 - Some emClarity funcitons will use this space too iff there is enough memory available.

Note that the mem avail is queried at runtime, so this could be a problem TODO

################################################################################ ################################################################################

NEW section to automatically create and delete a tmp cache dir.

Default to /tmp if the following doesn't workspace

MAX_MEM=0 MAX_FS='' EMC_CACHE_DIR='' EMC_CACHE_MEM=''

"emClarity_1_5_0_2_v19a" 117L, 3837C

Can I get some help in this trouble?

Best regards, Si Hoon Park

bHimes commented 3 years ago

It looks like you are running as root user inside a conda environment. Using conda should be fine, but why are you running as root?? I think this is probably an unwise idea

Did you run any command for emClarity? Try

emClarity_1_5_0_2_v19a check

Have you looked at the tutorial?

Ben

On Sat, Mar 6, 2021 at 8:11 PM whynotcat notifications@github.com wrote:

Dear bHimes, I am a beginner in cryo-tomography and matlab, morever emClarity, I got a trouble in installing of emClarity, like this

(base) [root@lsb bin]# sh emClarity_1_5_0_2_v19a Found tmpfs /dev/shm with max mem 131914048 bytes using this for MCR_CACHE_ROOT

##############

Created a tmp MCR_CACHE locally at /dev/shm/emC_tmp_28475
Available mem is 125.803 GB
Started emC_memClean to make sure it removed in the event of a crash.
Default kill time is a max of 10080 minutes

##############

Index exceeds the number of array elements (1).

Error in emClarity (line 39) MATLAB:badsubscript

I tried to install emClarity like this,

[shp@lsb bin]# vi emClarity_1_5_0_2_v19a

!/bin/bash

When this script is invoked, record the PID so that the EMC_tmpDir is deleted even in the event of a crash. (With program script added from EMC_tmpDir.sh)

thisPID=$$

Please modify this line to point to the text file in your MCR root

where you pasted the lines suggested to add to LD_LIBRARY_PATH during

install.

MCR_BASH="/work/thirdParty/MATLAB/mcr_bash.sh"

MCR_BASH=/usr/local/matlab_2019a/v96/mcr_bash.sh

Please modify this line to point to the install for emClarity binary

emClarity_ROOT=/work/emClarity

emClarity_ROOT=/home/shp/emclarity_1.5.0.2/bin This is added in the middle of the emClarity run script. It does the following. 1 - check for temporary file systems so that some disk i/o can instead be kept in memory. 2 - minimally the MCR_CACHE_ROOT is set there (formerly .mcrCarch_9.3 which is default) This avoids the problem where parallel pools are dying due to either slow filesystems or conflicts with other parpools from competing nodes. 3 - Fall back to $TMPDIR or /tmp if no tmpfs is found. 4 - Some emClarity funcitons will use this space too iff there is enough memory available. Note that the mem avail is queried at runtime, so this could be a problem TODO

################################################################################

################################################################################ NEW section to automatically create and delete a tmp cache dir. Default to /tmp if the following doesn't workspace

MAX_MEM=0 MAX_FS='' EMC_CACHE_DIR='' EMC_CACHE_MEM='' "emClarity_1_5_0_2_v19a" 117L, 3837C

Can I get some help in this trouble?

Best regards, Si Hoon Park

— 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/133, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAXPLGDMRPWTE2S2MEMPMPTTCLHC3ANCNFSM4YXJO2FQ .

--

Benjamin Himes, PhD

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

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

whynotcat commented 3 years ago

Dear Ben, Thank you for kind advice, I am re-trying to install emClarity with deactivating the conda in my local account.

I saw the , but emClarity_1_5_0_2_v19a check was not found like this;

[shp@lsb bin]$ ls docs emClarity_1_5_0_2 emClarity_1_5_0_2_v19a emClarity_1_5_0_2_v19a_2 logFile [shp@lsb bin]$ emClarity_1_5_0_2_v19a check bash: emClarity_1_5_0_2_v19a: command not found...

I also fixed mcr_bash.sh file, but it was not worked. I tried to install emClarity using sh command, is it wrong command?

(base) [shp@lsb bin]$ conda deactivate [shp@lsb bin]$ sh emClarity_1_5_0_2_v19a Found tmpfs /dev/shm with max mem 131914044 bytes using this for MCR_CACHE_ROOT

##############

    Created a tmp MCR_CACHE locally at /dev/shm/emC_tmp_29338
    Available mem is 125.803 GB
    Started emC_memClean to make sure it removed in the event of a crash.
    Default kill time is a max of 10080 minutes

##############

/usr/local/matlab_2020b/v99/mcr_bash.sh: line 1: /usr/local/matlab_2020b/v99/runtime/glnxa64:/usr/local/matlab_2020b/v99/bin/glnxa64:/usr/local/matlab_2020b/v99/sys/os/glnxa64:/usr/local/matlab_2020b/v99/extern/bin/glnxa64: Nuch file or directory /home/shp/emclarity_1.5.0.2/bin/emClarity_1_5_0_2: error while loading shared libraries: libmwlaunchermain.so: not open shared object file: No such file or directory

Sincerely, Si Hoon Park

whynotcat commented 3 years ago

Dear Ben, I tried emclarity check like this; but I still troubled in just install.. Thank you for concerning.

[shp@lsb bin]$ ./emClarity_1_5_0_2_v19a check Found tmpfs /dev/shm with max mem 131735060 bytes using this for MCR_CACHE_ROOT

##############

    Created a tmp MCR_CACHE locally at /dev/shm/emC_tmp_16836
    Available mem is 125.632 GB
    Started emC_memClean to make sure it removed in the event of a crash.
    Default kill time is a max of 10080 minutes

##############

Error using diary logFile/emClarity.logfile: File not found.

Error in emClarity (line 47)

MATLAB:fileio:fileNotFound

bHimes commented 3 years ago

Hmm, that's one I've never seen before. Do you have anyone in your lab or department who has some (U)Linux skills? It looks like you need some help with getting things installed correctly.

I've done as much as I can to make everything self contained and reasonably easy to install. I'm afraid I can't help to trouble shoot this with you.

whynotcat commented 3 years ago

Dear Ben, Thank you for reply. I will solve my problem by contacting someone near my lab. Thanks!

Best regards, SH

bHimes commented 3 years ago

Thank you!