[CP2K-user] [CP2K:18669] Re: Error in compiling Cp2k with PLUMED

[Krack Matthias]

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<mailto: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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