Yambo Community Forum

Dear All,
I am not a deep expert of Linux. I tried installing YAMBO on my machine using this string

./configure --with-netcdf-include=/home/giacomo/src/net/include/ --with-netcdf-lib=/home/giacomo/src/net/lib/ --with-iotk=/home/giacomo/src/espresso-4.2/iotk/ --with-p2y=4.0 PFC=ifort FC=ifort FCFLAGS="-O2 -assume byterecl -g -traceback -nomodule -fpp -D__INTEL -D__FFTW -I../include -static" --enable-largedb --enable-dp --with-blas="-lblas -lg2c" --with-lapack=-llapack

then

make yambo

and

make interfaces

Everything seems to be correct. it seems that the compilation has been successful.

Now, I run a PW job. It is the example01 in the 4.2 release of espresso. A simple band calculation for bulk Si.
When i launch the ./p2y in order to obtain the yambo input, I get this message

[giacomo@domitianus silicon.save]$ p2y

__ __ _______ __ __ _______ _______
| | | || _ || |_| || _ || |
| |_| || |_| || || |_| || _ |
| || || || || | | |
|_ _|| || || _ | | |_| |
| | | _ || ||_|| || |_| || |
|___| |__| |__||_| |_||_______||_______|

<---> [01] P(W) 2 Y(ambo) Ver. 4.0
<---> DBs path set to .
<---> Index file set to data-file.xml
<---> Header/K-points/Energies...done
<---> Cell data...done
<---> Atomic data...done
<---> Symmetries...

[ERROR] STOP signal received while in :[01] P(W) 2 Y(ambo) Ver. 4.0
[ERROR] Non-symmorphic symmetry operations are not supported! Use nosym=.true.ed in PWSCF

I checked the list and understood the reason. Then I correct my PWSCF input accordingly and I obtain this other message

[giacomo@domitianus silicon.save]$ p2y

___ __ _____ __ __ _____ _____
| Y || _ || Y || _ \ | _ |
| | ||. | ||. ||. | / |. | |
\_ _/ |. _ ||.\_/ ||. _ \ |. | |
|: | |: | ||: | ||: | \|: | |
|::| |:.|:.||:.|:.||::. /|::. |
`--" `-- --"`-- --"`-----" `-----"

<---> [01] P(W) 2 Y(ambo) Ver. 4.0
<---> DBs path set to .
<---> Index file set to data-file.xml
<---> Header/K-points/Energies...done
<---> Cell data...done
<---> Atomic data...done
<---> Symmetries...[ID yes]...[INV no]...[TR yes]...[SI no]
<---> XC functional...Perdew & Zunger (xc)
<---> K-points mesh...done
<---> RL vectors...

[ERROR] STOP signal received while in :[01] P(W) 2 Y(ambo) Ver. 4.0
[ERROR]Error in qexml_read_planewaves IOTK error ierr: 1



Could anyone kindly help me to fix this problem?
I attach the config.log

Thanks in advance!
My very best
Giacomo


Giacomo Giorgi, PhD,
Department of Chemical System Engineering,
School of Engineering,
The University of Tokyo,
7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656

Hi Giacomo.

Well, I found several problems in linking the iotk in these days....(I'm going to post in a while again for the happiness of yamboers..)

I've read in a previous post on the forum, viewtopic.php?f=1&t=75 that you can even link the lib_iotk from version 4.0.5 and read safely the .save from espresso_4.1.1 version for example.
This case is tested and it works.

in your case, since the epsresso_4.2. is very new, maybe there are still some instabilities with that.
I suggest you to stay on the previous version of espresso for the moment.

ciao, have fun!
federico.

Hi Giacomo

another comment: use force_symmorphic=.true. instead of nosym=.true. if you have a version of PWSCF
more recent than 4.0.5.

A question: did you use wf_collect=.true. in your PWSCF input?
if not use it.

cla

claudio wrote: A question: did you use wf_collect=.true. in your PWSCF input?
if not use it.

Looks like the problem to me: check that there is a file gvectors.dat inside the .save directory.
If there is, the problem lies elsewhere...
Conor

Dear Conor,
yes there is that gvectors.dat file.....
But now by changing the lib_iotk to those of the 4.1.3 and adding wf_collect=.true. and force_symmorphic=.true. in the PW input
the yambo input seems to be created correctly by "./p2y"

What do you mean for "elsewhere"? Are there additional instructions for debugging the compilation?

My very best,
Giacomo

Giacomo Giorgi, PhD,
Department of Chemical System Engineering,
School of Engineering,
The University of Tokyo,
7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656

Dear Giacomo,

giacsport wrote: and adding wf_collect=.true.

No other problems - this is all you had to do. Let us know if you run into problems immediately with running yambo, though.
Regards,
Conor

Dear Conor,
thanks a lot for your availability!

Very best
G

P.S.: One more question (hopefully the last....) if I can.... for the parallel installation (open-mpi) I used the same script

./configure --with-netcdf-include=/home/giacomo/src/net/include/ --with-netcdf-lib=/home/giacomo/src/net/lib/ --with-iotk=/home/giacomo/src/espresso-4.1.3-mpi/iotk --with-p2y=4.0 PFC=mpif90 FC=ifort FCFLAGS="-O2 -assume byterecl -g -traceback -nomodule -fpp -D__MPI" --enable-largedb --enable-dp --with-blas="-lblas -lg2c" --with-lapack=-llapack --with-mpi

changing thus PFC=ifort -> PFC=mpif90
and adding "--with-mpi"

the compilation seems to be successful

then "make yambo" and "make interfaces"

but when I launch the "./p2y" I have

[giacomo@domitianus bin]$ ./p2y
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
p2y 000000000041B0D7 Unknown Unknown Unknown
p2y 000000000041BDB2 Unknown Unknown Unknown
p2y 0000000000419CEA Unknown Unknown Unknown
p2y 000000000052A7D6 Unknown Unknown Unknown
libc.so.6 000000363F21C40B Unknown Unknown Unknown
p2y 000000000041992A Unknown Unknown Unknown

And honestly I am not able to figure out the reason.
Have you got some hints to suggest me?

Still excuse me for the stress!


Thanks!
Ciao!
Giacomo

Giacomo Giorgi, PhD,
Department of Chemical System Engineering,
School of Engineering,
The University of Tokyo,
7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656

Dear Conor,
please ignore my previous message.... I think I fixed the bug on my own!

Thanks in any case for your availability!


Very best

Giacomo


Giacomo Giorgi, PhD,
Department of Chemical System Engineering,
School of Engineering,
The University of Tokyo,
7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656