great!
may I get help please on another issue, if it is okay @ vperetroukhin, @olibclarke
meanwhile I updated my current v4.2.1 to v4.6
After upgradation, I can’t open any of my project/workspace!
Is there anything else I will have to do to see the projects/workspaces?
Cheers
Saif
@SaifCam I created a new topic to match the topic of your post.
Please can you
- perform the steps a complete/confirmed shutdown of CryoSPARC
- then, try
cryosparcm start
If you still can not access your project, please post the outputs of these commands
ps -eo pid,ppid,start,command | grep -e cryosparc_ -e mongo
ls -l /tmp/cryosparc*sock /tmp/mongo*sock
cryosparcm log update | tail -n 60
cryosparcm log supervisord | tail -n 30
cryosparcm status | grep -v LICENSE
Thanks @SaifCam for responding.
From your response, it appears that your CryoSPARC instance is running on a computer where many other CryoSPARC instances are also running. To avoid interference with the assigned port ranges of other CryoSPARC instances running on the same computer, changing the assigned port range of any CryoSPARC instance has to be carefully coordinated.
Have you been assigned a network port range that is guaranteed to not overlap with the port ranges of other CryoSPARC instances on the computer? If so, what is the number of the port at the beginning of that range?
What are the outputs of these commands
grep -v LICENSE /net/flash/flash/sislam/cryosparc/cryosparc_master/config.sh
cryosparcm log database | tail -n 40
(To preserve the privacy of other others on your computer, I have removed your response.)
Hi
before updating, the CS was on port 39900. After I updated to v4.6.0 and when I could not see the database, I changed the port to 39940.
Here is the output from running the script you suggested:
flash_sislam> grep -v LICENSE /net/flash/flash/sislam/cryosparc/cryosparc_master/config.sh
# Instance Configuration
export CRYOSPARC_MASTER_HOSTNAME="flash.lmb.internal"
export CRYOSPARC_DB_PATH="/net/flash/flash/sislam/cryosparc/db"
export CRYOSPARC_BASE_PORT=39940
export CRYOSPARC_DB_CONNECTION_TIMEOUT_MS=40000
export CRYOSPARC_FORCE_HOSTNAME=true
# Security
export CRYOSPARC_INSECURE=false
export CRYOSPARC_DB_ENABLE_AUTH=true
# Cluster Integration
export CRYOSPARC_CLUSTER_JOB_MONITOR_INTERVAL=10
export CRYOSPARC_CLUSTER_JOB_MONITOR_MAX_RETRIES=1000000
# Project Configuration
export CRYOSPARC_PROJECT_DIR_PREFIX='CS-'
# Development
export CRYOSPARC_DEVELOP=false
# Other
export CRYOSPARC_CLICK_WRAP=true
flash_sislam> cryosparcm log database | tail -n 40
----------------------------------------------------------------------------
Open MPI has detected that a parameter given to a command line
option does not match the expected format:
Option: n
Param: XXXmpinodesXXX
This is frequently caused by omitting to provide the parameter
to an option that requires one. Please check the command line and try again.
----------------------------------------------------------------------------
finger: Command not found.
Fatal Python error: init_interp_main: failed to update the Python config
Python runtime state: core initialized
ValueError: character U+656e512d is not in range [U+0000; U+10ffff]
Current thread 0x000014ecdf622d80 (most recent call first):
<no Python frame>
* RELION 4.0 JOB ENVIRONMENT *
PATH TO mpiexec: /public/EM/OpenMPI/openmpi-4.0.1/build/bin/mpiexec
PATH TO relion_refine_mpi: /public/EM/RELION/relion-4.0-dev/build/bin/relion_refine_mpi
LIBRARIES FOR relion_refine_mpi:
linux-vdso.so.1 (0x00007fffe9d60000)
/net/flash/flash/sislam/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/libpython3.10.so (0x00001469e04e0000)
libcufft.so.11 => /public/EM/CUDA/cuda-12.0/lib64/libcufft.so.11 (0x00001469d6f04000)
libmpi.so.40 => /public/EM/OpenMPI/openmpi-4.0.1/build/lib/libmpi.so.40 (0x00001469d6bf1000)
libdl.so.2 => /lib64/libdl.so.2 (0x00001469d69ed000)
libtiff.so.5 => /lib64/libtiff.so.5 (0x00001469d6774000)
libfftw3.so.3 => /public/EM/RELION/relion-4.0-dev/external/fftw/lib/libfftw3.so.3 (0x00001469d63ed000)
libfftw3f.so.3 => /public/EM/RELION/relion-4.0-dev/external/fftw/lib/libfftw3f.so.3 (0x00001469d5fda000)
libcurand.so.10 => /public/EM/CUDA/cuda-12.0/lib64/libcurand.so.10 (0x00001469cfb71000)
libpng16.so.16 => /lib64/libpng16.so.16 (0x00001469cf93c000)
libjpeg.so.62 => /lib64/libjpeg.so.62 (0x00001469cf6d3000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00001469cf4b3000)
librt.so.1 => /lib64/librt.so.1 (0x00001469cf2ab000)
libstdc++.so.6 => /public/gcc/8_3_0/lib64/libstdc++.so.6 (0x00001469cef28000)
libm.so.6 => /lib64/libm.so.6 (0x00001469ceba6000)
libgomp.so.1 => /public/gcc/8_3_0/lib64/libgomp.so.1 (0x00001469ce978000)
libgcc_s.so.1 => /public/gcc/8_3_0/lib64/libgcc_s.so.1 (0x00001469ce760000)
libc.so.6 => /lib64/libc.so.6 (0x00001469ce39b000)
/lib64/ld-linux-x86-64.so.2 (0x00001469e087d000)
libutil.so.1 => /lib64/libutil.so.1 (0x00001469ce197000)
libopen-rte.so.40 => /public/EM/OpenMPI/openmpi-4.0.1/build/lib/libopen-rte.so.40 (0x00001469cdedd000)
libopen-pal.so.40 => /public/EM/OpenMPI/openmpi-4.0.1/build/lib/libopen-pal.so.40 (0x00001469cdbcf000)
libz.so.1 => /lib64/libz.so.1 (0x00001469cd9b7000)
libjbig.so.2.1 => /lib64/libjbig.so.2.1 (0x00001469cd7ab000)
RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE: /public/EM/SIDESPLITTER/sidesplitter_wrapper.sh
SIDESPLITTER: /public/EM/SIDESPLITTER/sidesplitter
RUN STARTED AT Sun 22 Sep 22:45:06 BST 2024
-----------------------------------------------------------
-----------------------------------------------------------
RUN FINISHED AT 1727041506
ELAPSED WALL CLOCK TIME: 0
Thanks @SaifCam for this information.
As you could not “see” the database (for a reason unknown), I am not sure what effect an attempted change of the CryoSPARC port range may have. The database log may I have additional information.
I observed in your earlier response (which is no longer shown) that a database socket file corresponding to the old port range starting at 39900 was still present.
What are the outputs of these commands:
lsof /tmp/mongodb-39901.sock
ps -u sislam -o pid,ppid,start,command | grep -e cryosparc -e mongo
The command
cryosparcm log database | tail -n 40
may be incompatible with the environment at the flash_sislam> prompt. This could affect you in at least two ways:
- The command’s expected output is not available for analysis. You may instead try the command
tail -40 /net/flash/flash/sislam/cryosparc/cryosparc_master/run/database.log - Other commands, including CryoSPARC (re-)configuration commands, may similarly fail or have unexpected results.
You may want to ask you IT support for suggestions on how to run commands like
cryosparcm log database | tail -n 40
such that they produce the expected output, in this case, the final forty lines of stdout of the command
cryosparcm log database