yambo: command not found

[marsusi]

Dear Myrta,

So many thanks for quick respons.
Again it doesn't work. Then I noticed did not installed HDF5 libraries before netcdf. So installed it by typing:
sudo apt-get install libhdf5-serial-dev hdf5-tools
then mading yambo clean and configured it. This time make procedure took more time, and at the end received this error message:

(.text+0x1f6): undefined reference to `curl_easy_setopt'
/home/farah/local/yambo-3.4.1/lib/libnetcdf.a(liboc_la-curlfunctions.o):(.text+0x26f): more undefined references to `curl_easy_setopt' follow
collect2: ld returned 1 exit status
make[1]: *** [yambo] Error 1
make[1]: Leaving directory `/home/farah/local/yambo-3.4.1/driver'
make: *** [yambo] Error 2

Many thanks again for your helps.

Marsusi.

Marsusi.

[myrta gruning]

Hallo

Please uninstall hdf5 it is going to make things even more difficult. You do not need that anyway.
Just try to fix the issue netcdf first.

In the directory where the SAVE is can you

~>ls -ltr
and
~>ls -ltr SAVE

and post the result, just to be sure yambo can actually enter in the directory and see the files.

Best
m

[marsusi]

Dear Myrta,

Thanks so much for your quick response.
I noticed that didn't build HDF5 before netcdf. So built its libraries by typing: sudo apt-get install libhdf5-serial-dev, and reinstalled netcdf. Then configured yambo as your proposed option. This time making procedure took more time, but gave this error message:
(.text+0x1f6): undefined reference to `curl_easy_setopt'
/home/farah/local/yambo-3.4.1/lib/libnetcdf.a(liboc_la-curlfunctions.o):(.text+0x26f): more undefined references to `curl_easy_setopt' follow
collect2: ld returned 1 exit status
make[1]: *** [yambo] Error 1
make[1]: Leaving directory `/home/farah/local/yambo-3.4.1/driver'
make: *** [yambo] Error 2

Thanks for your helps.

Marsusi.

[myrta gruning]

Hallo

You do not need hdf5. Please uninstall it. It is not fixing your problem, but adding more.

Can you verify please the permissions of the SAVE directory as I asked you in the previous post?

Maybe it is just that the permissions of the directory are not OK.

Best
m

[marsusi]

Dear Myrta,

I removed it, netcdf was not working more. So I built a netcdf-4.3.2 in my /home/local directory. This time no problem with making yambo. but again not recognizes SAVE directory.
Please see the result of ls -ltr:
ls -ltr
total 8
drwxr-xr-x 2 farah farah 4096 Apr 6 2013 Inputs
drwxr-xr-x 2 farah farah 4096 Apr 6 2013 SAVE

ls -ltr SAVE
total 6132
-rw-r--r-- 1 farah farah 557040 Apr 6 2013 ns.wf_fragments_9_1
-rw-r--r-- 1 farah farah 557040 Apr 6 2013 ns.wf_fragments_8_1
-rw-r--r-- 1 farah farah 557040 Apr 6 2013 ns.wf_fragments_7_1
-rw-r--r-- 1 farah farah 557040 Apr 6 2013 ns.wf_fragments_6_1
-rw-r--r-- 1 farah farah 557040 Apr 6 2013 ns.wf_fragments_5_1
-rw-r--r-- 1 farah farah 557040 Apr 6 2013 ns.wf_fragments_4_1
-rw-r--r-- 1 farah farah 557040 Apr 6 2013 ns.wf_fragments_3_1
-rw-r--r-- 1 farah farah 557040 Apr 6 2013 ns.wf_fragments_2_1
-rw-r--r-- 1 farah farah 557040 Apr 6 2013 ns.wf_fragments_1_1
-rw-r--r-- 1 farah farah 557044 Apr 6 2013 ns.wf_fragments_10_1
-rw-r--r-- 1 farah farah 4096 Apr 6 2013 ns.wf
-rw-r--r-- 1 farah farah 60504 Apr 6 2013 ns.kb_pp_fragment_9
-rw-r--r-- 1 farah farah 60504 Apr 6 2013 ns.kb_pp_fragment_8
-rw-r--r-- 1 farah farah 60504 Apr 6 2013 ns.kb_pp_fragment_7
-rw-r--r-- 1 farah farah 60504 Apr 6 2013 ns.kb_pp_fragment_6
-rw-r--r-- 1 farah farah 60504 Apr 6 2013 ns.kb_pp_fragment_5
-rw-r--r-- 1 farah farah 60504 Apr 6 2013 ns.kb_pp_fragment_4
-rw-r--r-- 1 farah farah 60504 Apr 6 2013 ns.kb_pp_fragment_3
-rw-r--r-- 1 farah farah 60504 Apr 6 2013 ns.kb_pp_fragment_2
-rw-r--r-- 1 farah farah 60508 Apr 6 2013 ns.kb_pp_fragment_10
-rw-r--r-- 1 farah farah 60504 Apr 6 2013 ns.kb_pp_fragment_1
-rw-r--r-- 1 farah farah 4096 Apr 6 2013 ns.kb_pp
-rw-r--r-- 1 farah farah 83320 Apr 6 2013 ns.db1

Thanks.

[myrta gruning]

Thank you.
So the directory is accessible.
You compiled netcdf.
Did you use the same compilers as for yambo?
Was the netcdf recognized by the configure?
Are you sure you are using the last compiled version of yambo? Try to give the full path to the yambo executable.

I confess I am puzzled. I would expect problems from netcdf with configuring and compiling, not when executing.

m

[marsusi]

Dear Myrta,

Thanks again.
>>Did you use the same compilers as for yambo?
For both yambo and netcdf: FC=mpif90, CC=gcc
>>Was the netcdf recognized by the configure?
Yes! NETCDF/HDF5/Large Files in report.
>>Are you sure you are using the last compiled version of yambo?
I have used yambo-3.4.1.
>>Try to give the full path to the yambo executable.
It doesn't still work by executing from the full path ~/yambo/bin.
Also gcc version is 4.6.3, if it can help.

Thanks.

[myrta gruning]

Dear Marsusi

did you try to see if the interfaces (a2y or p2y) work?
and if they produce SAVE/ns.* or SAVE/s.* files?

There are example input files for DFT calculations that you can use in the tutorial page.

m