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run yambo

https://www.yambo-code.eu/forum/viewtopic.php?t=167

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Re: run yambo

Posted: Sun Apr 11, 2010 8:48 am
by sdwang
andrea marini wrote:
sdwang wrote: and NETCDF is compiled with ./configure FC=ifort prefix==/home/sdwang/netcdf/, it seems right.
But "yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)" also appears.
1. in the lib and include directories there are some directories including:
./lib/libnetcdf_c++.a
./lib/libnetcdf.a
./config/netcdf_f90.m4
./include/netcdf.mod
./include/netcdf.h
./include/netcdf.inc
./include/netcdfcpp.h
./include/netcdf.hh
2.ls -R result:

[sdwang@n32 bulk_silicon]$ ls -R
.:
experiment.dat README SAVE

./SAVE:
database_DB1_NETCDF_format database_WF_NETCDF_format db1 ns.wf

Shudong Wang
Southeast University in Nanjing,China
This is very strange. If you compiled with NETCDF support then you should be able to read the databases. So let's move step by step
  1. Do a make clean_all and Post the list of files in the lib and include directories immediately after the configure. You should see something like

    Code: Select all

    ./lib/libnetcdf_c++.a
./lib/libnetcdf.a
./config/netcdf_f90.m4
./include/netcdf.mod
./include/netcdf.h
./include/netcdf.inc
./include/netcdfcpp.h
./include/netcdf.hh
    If these files are present then yambo will be properly compiled.
  2. Are you sure you're running the code UP of the SAVE folder ? Please post the result of ls -R in the directory where you're running yambo.

Sdwang
Southeast University
Please.... we do need you COMPLETE name and your COMPLETE affiliation. I have no idea where the Southeast University and I am sure your name is not only sdwang! Edit these informations in your signature that you can access via your User control panel.

Re: run yambo

Posted: Sun Apr 11, 2010 6:51 pm
by andrea marini
Dear Shudong,

from the config.log I cannot understand too much. You passed the correct configure options but then yambo seems not to be able to read NETCDF files ? WHY ? But in my previous post I asked you to post other informations, and not the config.log files. Please read again my post and attach to your reply the list of files I asked you.

Re: run yambo

Posted: Sun Apr 11, 2010 8:11 pm
by Daniele Varsano
Dear Shudong,

in your SAVE directory you have the following files:
./SAVE:
database_DB1_NETCDF_format database_WF_NETCDF_format db1 ns.wf
thisi is not correct as you should have:
ns.wf ns.db1

i.e. the databses containing the electronic structure and the wavefunctions in the netcdf format (which are indicated by ns)
now I think you just mispelled the file ns.db1, as you have in your directory a db1 file. This should be the reason why
yambo does not find it. Just rename such file and it should work.

BTW: if you don't want to write your affiliation in each post, you can easily fill the signature in your profile.

Best,

Daniele

Re: run yambo

Posted: Mon Apr 12, 2010 5:38 am
by sdwang
I am very sorry.It does not work at all.Like as :
[sdwang@n33 bulk_silicon]$ /home/sdwang/yambo-3.2.1-r.448/bin/yambo

yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)

Shudong Wang

Southeast University in Nanjing ,China

Re: run yambo

Posted: Mon Apr 12, 2010 8:17 am
by Daniele Varsano
Dear Shadong,

have you renamed your file "db1" in "ns.db1" ?

when you have used the ncgen command, the netcdf libraries where
compiled with the same compiler you are compiling yambo?

Best,

Daniele

Re: run yambo

Posted: Sat Apr 24, 2010 10:34 am
by sdwang
Dear:
Is the Netcdf must be installed if I want to use Yambo? Is the yambo compiled and used sepatately?

Shudong Wang

Southeast University in Nanjing,China.

Re: run yambo

Posted: Sat Apr 24, 2010 10:43 am
by andrea marini
sdwang wrote: Is the Netcdf must be installed if I want to use Yambo? Is the yambo compiled and used sepatately?
Yambo can be compiled and run without linking to NETCDF libraries. However if you want to read the databases provided with the source you must link against netcd librarires. These need to be compiled separatevly.

Re: run yambo

Posted: Sun Apr 25, 2010 6:01 am
by sdwang
Dear:

I complie Yambo without link to Netcdf on RedHat 3.4.4-2 version.There is no error after configure,but when type "make all" ,it appears:

.....
>>>[Linking yambo]<<<
make[1]: Entering directory `/home/sdwang/yambo-3.2.1-r.448/driver'
yambo_driver.F
driver.o(.text+0x430): In function `main':
/home/sdwang/yambo-3.2.1-r.448/driver/driver.c:98: multiple definition of `main'
/usr/local/intel/fce/9.0/lib/for_main.o(.text+0x0): first defined here
ld: Warning: size of symbol `main' changed from 70 in /usr/local/intel/fce/9.0/lib/for_main.o to 2985 in driver.o
/usr/local/intel/fce/9.0/lib/for_main.o(.text+0x2e): In function `main':
: undefined reference to `MAIN__'
make[1]: *** [yambo] Error 1
make[1]: Leaving directory `/home/sdwang/yambo-3.2.1-r.448/driver'
make: *** [yambo] Error 2

%%%%%%%%%%%%%%%%%%%%%%
I compile with: ./configure --with-iotk=/home/sdwang/espresso-3.2.3/iotk/ --with-p2y=3.2 --with-mpi=/usr/local/mpich/lib/libmpichf90.a FC=mpif90
result: [SYS] linux@x86_64
# [SRC] /home/sdwang/yambo-3.2.1-r.448
# [BIN] /home/sdwang/yambo-3.2.1-r.448/bin
# [FFT] Goedecker Fast Fourier transform with 0 cache
#
# [ ] Double precision
# [X] Redundant compilation
# [X] MPI
# [X] PW (3.2) support
# [ ] ETSF I/O support
# [ ] SCALAPACK
# [ ] NETCDF/Large Files
# [XX ] Built-in BLAS/LAPACK/LOCAL
#
# [ CPP ] gcc -E -P
# [ C ] gcc -g -O2 -D_C_US -D_FORTRAN_US
# [MPICC] mpicc -g -O2 -D_C_US -D_FORTRAN_US
# [ F90 ] mpif90 -O
# [MPIF ] mpif90 -O
# [ F77 ] mpif90 -O
# [Cmain]
# [NoOpt]
#
# [ MAKE ] make
# [EDITOR] vi

gcc version 3.4.4
ifort 9.0
Yambo: yambo-3.2.1-r.448
Architecture:x86_64_redhat
Where is my problem?
Thanks!


S.D.Wang
Southeast University in Nanjing,china

Re: run yambo

Posted: Sun Apr 25, 2010 9:38 am
by claudio
The problem is that YAMBO is not recognizing mpif90 as intel fortran compiler you have to change
your configuration line as:

./configure --with-iotk=/home/sdwang/espresso-3.2.3/iotk/ --with-p2y=3.2 --with-mpi=/usr/local/mpich/lib/libmpichf90.a FC=ifort F77=ifort PFC=mpif90

Re: run yambo

Posted: Mon Apr 26, 2010 12:53 pm
by Conor Hogan
Dear Shudong,
Before you give up on the netcdf-linked yambo completely, can you post the result of the command:

ls -l SAVE

from the directory where you run yambo, so that we can check the contents of the SAVE directory?
It is possible that nearly everything you have done is correct, with just some small mistake.
Regards,
Conor
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