Compiling error yambo_nl

[aziz.ogutlu]

Hi there all,
I'm compiling yambo 5.1.1 on Rocky Linux 8 with gcc 9.4.0 with commands below:

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./configure --prefix=/opt/ohpc/pub/apps/yambo/5.1.1
make all

I'm also getting this error below:

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Error: There is no specific subroutine for the generic ‘it’ at (1)
        [driver] yambo_nl (checking work to be done)
yambo_nl linking failed. Check log/compile_yambo_nl.log

Could you help on this?

Thanks,
Aziz

[Davide Sangalli]

Dear Aziz,
this is probably an issue due to the switching from single precision (default for most of the yambo executables) to double precision (needed by yambo_nl and ypp_nl) at compilation time.
I suppose, from the log folder, that all the executables were compiled, with the exception of yambo_nl and ypp_nl.

1) First, if you do not need to perform non linear optics simulations, then you are fine.
You can just use the executables that you find in the bin folder.

2) Instead, if you need to perform non linear optics simuilations you have 2 options:
With option 2.a you will have the standard executables in single precision, which uses less memory, but which maybe also subject to rounding errors
With option 2.b you wull have all the executables compiled in double precision.

2.a) A workaround.
From the source folder just run

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touch */*/*.F
make nl-project -j

2.b) Recompile everything in double precision (I also added an option to store the external libraries in a separate folder)

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make distclean
./configure --prefix=/opt/ohpc/pub/apps/yambo/5.1.1 --enable-dp --with-extlibs-path=/opt/ohpc/pub/apps/yambo/ext-libs
make all -j

Best,
D.

[aziz.ogutlu]

Dear Davide,
Thank you for your response.
When I tried to use 2b solution, I got this error below:

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make[2]: *** [/data/yambo-5.1.1/config/mk/local/rules.mk:9: INIT_load.o] Error 1
make[2]: *** Waiting for unfinished jobs....
        [src/interface] INIT
        [src/interface] INIT_check_databases
        [src/interface] INIT_read_command_line
Error: There is no specific subroutine for the generic ‘it’ at (1)
Error: There is no specific subroutine for the generic ‘it’ at (1)

When I tried to use 2a solution, I got this error below:

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Fatal Error: Cannot open module file ‘netcdf.mod’ for reading at (1): No such file or directory
        [driver] yambo_nl (checking work to be done)
yambo_nl linking failed. Check log/compile_yambo_nl.log
Fatal Error: Cannot open module file ‘netcdf.mod’ for reading at (1): No such file or directory
make[1]: *** [config/mk/global/actions/compile_yambo.mk:42: yambo_nl] Error 1
yambo_nl build failed

[Davide Sangalli]

Something is strange here.

Are you sure you did

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make distclean

before re-running the configure in option 2.b ?

Best,
D.

[aziz.ogutlu]

Dear Davide,

Sure I did make distclean before configure.

But after that I started from untar archive, I could compile Yambo.

Thanks for your help,

Best regards,
Aziz

[myyambouser]

Hello,

I'm trying to compile Yambo 5.1.0 on Linux 7 with gcc 10.3.0 in parallel with the commands below:

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 ./configure --host="x86_64-pc-linux-gnu" --build="x86_64-pc-linux-gnu" -enable-mpi --enable-open-mp  --enable-hdf5-par-io --enable-msgs-comps --enable-time-profile --enable-memory-profile --with-blas-libs="-lopenblas"  --with-lapack-libs="-lopenblas" --with-libxc-path=$EBROOTLIBXC --with-fft-path=$EBROOTFFTW  --with-hdf5-path=$EBROOTHDF5 --with-netcdf-path=$EBROOTNETCDF --with-netcdff-path=$EBROOTNETCDFMINFORTRAN

I am facing different errors while compiling Yambo. Example: (conftest.c:9:10: fatal error: ac_nonexistent.h: No such file or directory) and (main: error: undefined reference to 'foobar')
I would appreciate your assistance to make this work.

Regards,
Richard.

[Davide Sangalli]

Dear Richard,
please add your signature in the setting of your user. This is a rule of the forum.

The errors you report from the config.log file are not a problem.
When you run the configure, it will try different operations to check what works and what does not work on your machine.
Some operation will fail and the configure will mark them as not correct on your machine.
From what I see, the configure procedure finishes correctly.

After that you can just run

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make core -j
make nl-project -j

and the code should be compiled.

Best,
D.

[myyambouser]

Thank you Davide for the prompt reply,
Currently i am also trying to build Yambo 5.1.1 on aarch64 architecture, but it fails during early configure phase:

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checking if the current OS is supported... no
configure: Platform <aarch64-unknown-linux-gnu> is not supported.
configure: Please contact the Yambo team at yambo@yambo-code.org
configure: providing either a list of compilers and options or
configure: a guest account on this machine.
configure: error: stopping

Machine cpu info:
Architecture: aarch64
Byte Order: Little Endian
CPU(s): 16
On-line CPU(s) list: 0-15
Thread(s) per core: 1
Core(s) per socket: 16
Socket(s): 1
NUMA node(s): 1
Vendor ID: ARM
Model: 1
Stepping: r1p1
BogoMIPS: 2100.00
L1d cache: 64K
L1i cache: 64K
L2 cache: 1024K
L3 cache: 32768K
NUMA node0 CPU(s): 0-15

Your assistance is highly appreciated.

[Davide Sangalli]

Unfortunately we do not yet support this kind of architecture.
There is work in progress in this direction however.
We will let you know as soon as there will be updates.