[CP2K-user] [CP2K:18670] Re: Error in compiling Cp2k with PLUMED

[Rajorshi Chattopadhyay]

Hi,

The -lpthread linker flag was already there in the arch file produced by
CP2k after the library installation step via the toolchain script. I also
checked that the path to libpthread is in the LIBRARY_PATH environment
variable.

On Sat, 15 Apr 2023 at 21:13, Krack Matthias <matthias.krack at psi.ch> wrote:

> Hi
>
>
>
> Did you try to add the linker flag “-lpthread”.
>
>
>
> HTH
>
>
>
> Matthias
>
>
>
> *From: *cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of
> Rajorshi Chattopadhyay <rajorshichat at gmail.com>
> *Date: *Saturday, 15 April 2023 at 01:07
> *To: *cp2k at googlegroups.com <cp2k at googlegroups.com>
> *Subject: *[CP2K:18667] Re: Error in compiling Cp2k with PLUMED
>
> Hello all,
>
>
>
> To provide some more information, I am trying to compile cp2k.ssmp and
> cp2k.sdbg with PLUMED. I have configured PLUMED with the disabled mpi
> option.
>
>
>
> On Fri, 14 Apr 2023 at 19:22, Rajorshi Chattopadhyay <
> rajorshichat at gmail.com> wrote:
>
> Hello all,
>
>
>
> I am trying to compile CP2k-9.1 with PLUMED 2.8.2. I could install PLUMED
> separately, but when I try to compile CP2k with PLUMED, I get the following
> error:
>
>
>
> /usr/bin/ld:
> /home/rajorshi/cp2k-9.1/tools/toolchain/install/libxsmm-1.17/lib/libxsmm.a(libxsmm_malloc.o):
> in function `libxsmm_xget_scratch_allocator':
>
> libxsmm_malloc.c:(.text.libxsmm_xget_scratch_allocator+0x111): undefined
> reference to `pthread_yield'
>
> /usr/bin/ld:
> /home/rajorshi/cp2k-9.1/tools/toolchain/install/libxsmm-1.17/lib/libxsmm.a(libxsmm_malloc.o):
> in function `libxsmm_xrelease_scratch':
>
> libxsmm_malloc.c:(.text.libxsmm_xrelease_scratch+0x101): undefined
> reference to `pthread_yield'
>
> /usr/bin/ld:
> /home/rajorshi/cp2k-9.1/tools/toolchain/install/libxsmm-1.17/lib/libxsmm.a(libxsmm_main.o):libxsmm_main.c:(.text.libxsmm_finalize+0xf1):
> more undefined references to `pthread_yield' follow
>
> collect2: error: ld returned 1 exit status
>
> make[3]: *** [/home/rajorshi/cp2k-9.1/obj/local/ssmp/all.dep:150:
> /home/rajorshi/cp2k-9.1/exe/local/grid_unittest.ssmp] Error 1
>
> make[2]: *** [/home/rajorshi/cp2k-9.1/Makefile:158: all] Error 2
>
> make[1]: *** [/home/rajorshi/cp2k-9.1/Makefile:140: ssmp] Error 2
>
> make[1]: *** Waiting for unfinished jobs....
>
> make[2]: *** [/home/rajorshi/cp2k-9.1/Makefile:158: all] Error 2
>
> make[1]: *** [/home/rajorshi/cp2k-9.1/Makefile:140: sdbg] Error 2
>
> make: *** [Makefile:135: all] Error 2
>
>
>
> I find that the libxsmm library was installed successfully in the previous
> step.
>
> I have attached the entire output of make and the arch file for reference.
>
> --
>
> With Regards,
>
> Rajorshi Chattopadhyay,
>
> PhD Researcher in Mineralogy/Crystallography,
>
> Institut für Geologie und Mineralogie,
>
> Universität zu Köln, Germany
>
>
>
>
>
>
> --
>
> With Regards,
>
> Rajorshi Chattopadhyay,
>
> PhD Researcher in Mineralogy/Crystallography,
>
> Institut für Geologie und Mineralogie,
>
> Universität zu Köln, Germany
>
>
>
> ​
>
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>


-- 
With Regards,
Rajorshi Chattopadhyay,
PhD Researcher in Mineralogy/Crystallography,
Institut für Geologie und Mineralogie,
Universität zu Köln, Germany

​

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