CP2K+OMEN

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Luca

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May 19, 2019, 3:57:10 PM5/19/19
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Dear developers

I am trying to install CP2K+OMEN by using the installer.sh script provided with the dft-transport sources.
Unfortunately, the installer does not finish his work since it crashes with the error:

--------------------------------------------------------------------------------------------------------
 build CP2K you should change directory:
  cd cp2k/makefiles/
  make -j 16 ARCH=local VERSION="sopt sdbg ssmp popt pdbg psmp"

arch files for GPU enabled CUDA versions are named "local_cuda.*"
arch files for valgrind versions are named "local_valgrind.*"
arch files for coverage versions are named "local_coverage.*"
./installer.sh: line 141: .../CP2K-OMEN/cp2k/cp2k/tools/toolchain/scripts/package_versions.sh: No such file or directory
--------------------------------------------------------------------------------------------------------

Could you please help me to overcome this issue?
Best Regards.

Luca 

Tiziano Müller

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May 20, 2019, 3:22:00 AM5/20/19
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Hi Luca,

the dft-transport code seems to be assuming the old CP2K directory
layout from when we were still using Subversion.

It might be enough to correct line 111 in the installer.sh to

cp2k_toolchainDIR=${cp2kDIR}/tools/toolchain

... and in lines 121, 130, 403 remove the `cp2k/` as well.

Best regards,
Tiziano
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Luca

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May 20, 2019, 4:21:43 AM5/20/19
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Dear Tiziano

thank you for your answer. Unfortunately, your hints do not fix the issue. The path to the cp2k sources is .../CP2K-OMEN/cp2k/cp2k/src.
I believe the reason is that the script package_versions.sh do not exist in the dir ../script.
Furthermore, that script is not even present in the entire cp2k dir.
Does anyone know the reason for that? Which is the cp2k release I have to use with OMEN? I am using the 6.1 

Best Regards.
Luca 

Tiziano Müller

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May 20, 2019, 6:48:24 AM5/20/19
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Hi Luca,

On 20.05.19 10:21, Luca wrote:
> Dear Tiziano
>
> thank you for your answer. Unfortunately, your hints do not fix the
> issue. The path to the cp2k sources is .../CP2K-OMEN/cp2k/cp2k/src. > I believe the reason is that the script package_versions.sh do not exist
> in the dir ../script.
> Furthermore, that script is not even present in the entire cp2k dir.
> Does anyone know the reason for that? Which is the cp2k release I have
> to use with OMEN? I am using the 6.1

in v6.1 the script should still be there:

https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh

But it seems that the script by default pulls from old SVN trunk which
is already missing the `package_versions.sh`.

You can proceed by either commenting out the SVN checkout part in OMEN's
`installer.sh` and make sure it uses the CP2K sources you provide or change

cp2kTRUNKorRELEASE="trunk"
cp2kRELEASEVER="4_1"

to

cp2kTRUNKorRELEASE="release"
cp2kRELEASEVER="6_1"

which should make the script pull version 6.1 from the old SVN (both
methods not tested by me).
In any what it seems you need some manual work to make the
`installer.sh` work again.

Best regards,
Tiziano
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Luca

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May 21, 2019, 4:07:04 AM5/21/19
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Dear Tiziano

thank you for your help. 
Best Regards
Luca 

Luca

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May 21, 2019, 5:09:35 AM5/21/19
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Dear Tiziano

I was able to compile libcp2k, but I was less lucky with omen.

I get the errors 

/usr/bin/ld: cannot find -lxsmmf
/usr/bin/ld: cannot find -lxsmm
/usr/bin/ld: cannot find -lderiv
/usr/bin/ld: cannot find -lint
/usr/bin/ld: cannot find -lxcf90
/usr/bin/ld: cannot find -lxc
/usr/bin/ld: cannot find -lfftw3
/usr/bin/ld: cannot find -lmpifort
/usr/bin/ld: cannot find -lopenblas

Could you please help me with this?

Bests
Luca

Tiziano Müller

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May 21, 2019, 7:05:50 AM5/21/19
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Hi Luca,

this means that the linker is unable to find the mentioned libraries [1].

Make sure you source the `setup` file from the toolchain (as instructed
by the toolchain script):

source [...]/cp2k/tools/toolchain/install/setup

which adds the library paths to the variable `$LD_LIBRARY_PATH` from
where the linker should pick them up.

Best regards,
Tiziano

[1]
https://stackoverflow.com/questions/16710047/usr-bin-ld-cannot-find-lnameofthelibrary
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Luca

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May 22, 2019, 3:07:41 AM5/22/19
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Dear Tiziano

yes, I forgot to source the setup. However, setting the environment does not seem to be enough for compiling omen.
The installer gets stuck now with:

DHAVE_MUMPS  -DHAVE_PEXSI    -lrt -ldl -lstdc++ -lgfortran -lmpifort -lopenblas
/CP2K-OMEN-GCC/cp2k/cp2k/lib/local/popt/libcp2k.a(xc_libxc.o): In function `__xc_libxc_MOD_libxc_lsd_eval':
/CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:631: undefined reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'
/CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:632: undefined reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'
/CP2K-OMEN-GCC/cp2k/cp2k/lib/local/popt/libcp2k.a(xc_libxc.o): In function `libxc_lsd_calc':
/CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:1621: undefined reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'
/CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:1622: undefined reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'
/CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:2281: undefined reference to `__xc_f03_lib_m_MOD_xc_f03_func_info_get_family'
/CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:1962: undefined reference to `__xc_f03_lib_m_MOD_xc_f03_mgga_exc'
/CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:1962: undefined reference to `__xc_f03_lib_m_MOD_xc_f03_mgga_exc'
/CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:1759: undefined reference to `__xc_f03_lib_m_MOD_xc_f03_gga_exc'
/CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:1759: undefined reference to `__xc_f03_lib_m_MOD_xc_f03_gga_exc'


Could you please help me again?

Bests
Luca 



 

Tiziano Müller

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May 22, 2019, 3:31:21 AM5/22/19
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Hi Luca,

I guess one or both of

-lxcf03 -lxc

are missing from the linker line.

Best regards,
Tiziano
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Luca

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May 22, 2019, 6:42:27 AM5/22/19
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Hi Tiziano

I added -lxcf03  (-lxc was already there) to the .mk file, but this does not solve the issue.

/CP2K-OMEN-GCC/cp2k/cp2k/tools/toolchain/install/libxc-4.0.3/lib/libxcf03.a(libxcf03_la-libxcf03.o): In function `__xc_f03_lib_m_MOD_xc_f03_functional_get_number':
/CP2K-OMEN-GCC/cp2k/cp2k/tools/toolchain/build/libxc-4.0.3/src/./libxc_master.F03:694: undefined reference to `xc_functional_get_number'
/CP2K-OMEN-GCC/cp2k/cp2k/tools/toolchain/install/libxc-4.0.3/lib/libxcf03.a(libxcf03_la-libxcf03.o): In function `__xc_f03_lib_m_MOD_xc_f03_functional_get_name':
/CP2K-OMEN-GCC/cp2k/cp2k/tools/toolchain/build/libxc-4.0.3/src/./libxc_master.F03:687: undefined reference to `xc_functional_get_name'
/CP2K-OMEN-GCC/cp2k/cp2k/tools/toolchain/install/libxc-4.0.3/lib/libxcf03.a(libxcf03_la-libxcf03.o): In function `__xc_f03_lib_m_MOD_xc_f03_func_get_info':
/CP2K-OMEN-GCC/cp2k/cp2k/tools/toolchain/build/libxc-4.0.3/src/./libxc_master.F03:680: undefined reference to `xc_func_get_info'
/CP2K-OMEN-GCC/cp2k/cp2k/tools/toolchain/install/libxc-4.0.3/lib/libxcf03.a(libxcf03_la-libxcf03.o): In function `__xc_f03_lib_m_MOD_xc_f03_func_end':


Bests
Luca 

Tiziano Müller

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May 22, 2019, 1:45:38 PM5/22/19
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Hi Luca,

can you make sure that the order is actually "-lxcf03 -lxc" (and not the
other way round)?

Because the error message actually changed.

Best,
Tiziano
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Luca

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May 23, 2019, 4:04:58 AM5/23/19
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Dear Tiziano

I thank you a lot for your help. I was able to compile the code although new issues have turned up.
I did the two available tests: the former related to the graphene transmission and the latter related to transport in a lithium chain.
The transmission calculation runs fine but it needs the same time both in serial and in parallel with 2 mpi procs. It is, instead,  much slower with 4 mpi processors. 
With the other test, the Lithium chain,  I get a segmentation fault. The last lines printed are :


--------------------------------------------------------------------------------
 KPOINTS| Number of kpoint groups                                              2
 KPOINTS| Size of each kpoint group                                            1
 KPOINTS| Number of kpoints per group                                         32

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 29677 RUNNING AT node165
=   EXIT CODE: 11
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
---------------------------------------------------------------------------------------------------------


Could you please give me other hints?

Bests
Luca 

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