Dear,
I am trying to do the "CTF estimation" in relion/3.1, and have questions.
1. With GCTF v1.18, I got random Phase shift searching that never ends.
Of course, I selected "No" for "Estimate phase shifts?" option.
The output is like
searching phase shift ...
Phase_shift def_U def_V Angle CCC
0.00 10334.94 10067.75 -6.85 146.473251
0.00 10334.78 10067.59 -7.02 146.472900
0.00 10334.78 10067.59 -7.02 146.472900
0.00 10334.78 10067.59 -7.02 146.472900
0.00 10334.78 10067.59 -7.02 146.472900
0.00 10334.78 10067.59 -7.02 146.472900
0.00 10334.78 10067.59 -7.02 146.472900
... {continue until it hits the wall time}
I used multi-GPUs and other GPUs that didn't get into this "forever phase searching" successfully process it.
It is random, so when I do a larger dataset, it is likely got into this.
A small dataset, for example, the relion tutorial dataset, runs fine without this issue.
If I resubmit the job manually, like
sbatch CtfFind/job00X/run_submit.script
then, it runs without the issue.
I think this could be a bug. Any comment would be very useful.
2. With CTFFIND-4.1, I got messages like
=========
A process has executed an operation involving a call to the
"fork()" system call to create a child process. Open MPI is currently
operating in a condition that could result in memory corruption or
other system errors; your job may hang, crash, or produce silent
data corruption. The use of fork() (or system() or other calls that
create child processes) is strongly discouraged.
The process that invoked fork was:
Local host: [[61523,0],17] (PID 99483)
If you are *absolutely sure* that your application will successfully
and correctly survive a call to fork(), you may disable this warning
by setting the mpi_warn_on_fork MCA parameter to 0.
==========
We use openmpi 4.0.3. It doesn't create any issues so far, but I like to know if it is known to be safe.
Thanks!
-Heechang
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