Dear Nick,
Thanks for your quick reply.
I have make a sample of k-points on the electrode. But the TSHS file of
electrode is calcualted on anothter cluster of which the OS is Suse. Due to
the memeory capacity, I have to use a large memeory cluster. But on this one,
the OS is Ubuntu. So I guess, the error may be caused by this. So I
recalculate the electrode on the new cluster. The task is in the queue. I hope
this can solve this problem. If it does not work, I will follow your
instruction step by step to figure out the reasion.
But another thing strange I have met is: in the mannul it saids the fdf is case
insensitive. And this is true in the suse cluster. But on the Ubuntu cluster,
it not the case. In Z-matrix declaration, the key word "Variables" is not
recognized, it must be "variables". Is this because Ubuntu?
Best regard.
Yours
Guangping Zhang
2013-10-10
发件人：Nick Papior Andersen <nickpap...@gmail.com>
发送时间：2013-10-10 08:48
主题：Re: [SIESTA-L] Bus error during Transiesta in trunk428
收件人："siesta-l@uam.es"<siesta-l@uam.es>
抄送：
The only deallocation performed by node 0 is an array containing the atomic
species, I suspect you see the same error no matter the number of cores used?
It could mean a couple of things, the electrode TSHS is not fully populated
(i.e. erroneous), you did a Gamma-point electrode calculation, or that there is
an actual error in the communication.
Can you please supply your electrode and transiesta fdf files.
Could you please try and goto line 1055 of file Src/m_ts_electrode.F90 and add
this (right before the "call memory" line):
print*,allocated(isa),isa
and recompile/run and return the output to me?
Kind regards Nick
2013/10/10 zgp121 <zgp...@126.com>
Dear SIESTA users:
When I use 24 cores to run the TranSIESTA calculation using trunk 428, I got
the error like this:
/var/spool/slurmd/job1321828/slurm_script: line 12: 19218 Bus error mpirun
transiesta < trans-0.0.fdf > trans-0.0.log
And I also find the following message in trans-0.0.log:
Creating Green's function file for: left
WARNING: alloc-realloc-dealloc name mismatch
Name: elec_HS unknown
Size: -588. Bytes
Node: 0
Subsequent mismatches will not be reported
The system of the HPC is Ubuntu. And in the compiliation, Ifort(10.1.012),
MKL(10.0.2.018), OpenMPI(1.4.5) are used.
Can anyone figure out what is the problem?
Guangping Zhang
2013-10-10
