[Wien] A question about the Rkm

Sat Jan 9 22:07:24 CET 2016

Hi, Marks and Peter:

Thank you for your suggestions. About your reply, I have several follow-up questions. Actually, I’m using a intermediate cluster in my university, which has 16 cores and 64 GB memory on standard nodes. The calculation I’m doing is k-point but not MPI parallelized. From the :RKM flag I posted in my first email, I estimate that the matrix size I need for a Rkmax=5+ will be at least 40000. In my current calculation, the lapw1 program will occupy as large as 3GB on each slot (1 k point/slot). So I estimate the memory for each slot will be at least 12 GB. I have 8 k points so that 96 GB memory will be required at least (if my estimation is correct). Considering the current computation resources I have, this is way too memory demanding. On our clusters, there’s a 4 GB memory limit for each slot on standard node. Although I can submit request for high memory node, but their usages are very competitive among cluster users. Do you have any suggestions on accomplishing this calculation within the limitation of my cluster?

About the details of my calculation, the material I'm looking at is a hydrogen terminated silicon carbide with 56 atoms. A 1x1x14 k-mesh is picked for k-point sampling. The radius of 1.2 is achieved from setrmt_lapw actually. Indeed, the radius of hydrogen is too large and I’m adjusting its radius during the progress of optimization all the time. The reason why I have such a huge matrix is mainly due to size of my unit cell. I’m using large unit cell to isolate the coupling between neighboring nanowire.

Except for the above questions, I also met some problems in mpi calculation. By following Marks’ suggestion on parallel calculation, I want to test the efficiency of mpi calculation since I only used k-point parallelized calculation before. The MPI installed on my cluster is openmpi. In the output file, I get the following error:

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 LAPW0 END

lapw1c_mpi:19058 terminated with signal 11 at PC=2b56d9118f79 SP=7fffc23d6890.  Backtrace:
...
mpirun has exited due to process rank 14 with PID 19061 on
node neon-compute-2-25.local exiting improperly. There are two reasons this could occur:

1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.

2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"

This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
Uni_+6%.scf1up_1: No such file or directory.
grep: *scf1up*: No such file or directory

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

The job script I’m using is:

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
!/bin/csh -f
# -S /bin/sh
#
#$ -N uni_6
#$ -q MF
#$ -m be
#$ -M wenhao-hu at uiowa.edu<mailto:wenhao-hu at uiowa.edu>
#$ -pe smp 16
#$ -cwd
#$ -j y

cp $PE_HOSTFILE hostfile
echo "PE_HOSTFILE:"
echo $PE_HOSTFILE
rm .machines
echo granularity:1 >>.machines
while read hostname slot useless; do
    i=0
    l0=$hostname
    while [ $i -lt $slot ]; do
        echo 1:$hostname:2 >>.machines
        let i=i+2
    done
done<hostfile

echo lapw0:$l0:16 >>.machines

runsp_lapw -p -min -ec 0.0001 -cc 0.001 -fc 0.5
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Is there any mistake I made or something missing in my script?

Thank your very much for your help.

Wenhao

I do not know many compounds, for which an RMT=1.2 bohr for H makes any sense (maybe LiH). Use setrmt and follow the suggestion. Usually, H spheres of CH or OH bonds should be less than 0.6 bohr. Experimental H-position are often very unreliable.
How many k-points ? Often 1 k-point is enough for 50+ atoms (at least at the beginning), in particular when you ahve an insulator.
Otherwise, follow the suggestions of L.Marks about parallelization.

Am 08.01.2016 um 07:28 schrieb Hu, Wenhao:

Hi, all:

I have some confusions on the Rkm in calculations with 50+ atoms. In my wien2k,
the NATMAX and NUME are set to 15000 and 1700. With the highest NE and NAT, the
Rkmax can only be as large as 2.05, which is much lower than the suggested
value in FAQ page of WIEN2K (the smallest atom in my case is a H atom with
radius of 1.2). By checking the :RKM flag in case.scf, I have the following
information:

:RKM  : MATRIX SIZE 11292LOs: 979  RKM= 2.05  WEIGHT= 1.00  PGR:

With such a matrix size, the single cycle can take as long as two and half
hours. Although I can increase the NATMAX and NUME to raise Rkmax, the
calculation will be way slower, which will make the optimization calculation
almost impossible. Before making convergence test on Rkmax, can anyone tell me
whether such a Rkmax is a reasonable value?

If any further information is needed, please let me know. Thanks in advance.

Best,
Wenhao
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