<div dir="ltr">Hi,<div><br></div><div>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.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, 15 Apr 2023 at 21:13, Krack Matthias <<a href="mailto:matthias.krack@psi.ch">matthias.krack@psi.ch</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div class="msg4448274704660630580"> <div lang="en-CH" style="overflow-wrap: break-word;"> <div class="m_4448274704660630580WordSection1"> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11pt">Hi<u></u><u></u></span></p> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11pt"><u></u> <u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">Did you try to add the linker flag “-lpthread”.<u></u><u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">HTH<u></u><u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">Matthias<u></u><u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p> <div style="border-style:solid none none;border-top-width:1pt;border-top-color:rgb(181,196,223);padding:3pt 0cm 0cm"> <p class="MsoNormal" style="margin-right:0cm;margin-bottom:12pt;margin-left:36pt"> <b><span style="font-size:12pt;color:black">From: </span></b><span style="font-size:12pt;color:black"><a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a> <<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a>> on behalf of Rajorshi Chattopadhyay <<a href="mailto:rajorshichat@gmail.com" target="_blank">rajorshichat@gmail.com</a>><br> <b>Date: </b>Saturday, 15 April 2023 at 01:07<br> <b>To: </b><a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a> <<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a>><br> <b>Subject: </b>[CP2K:18667] Re: Error in compiling Cp2k with PLUMED<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt">Hello all,<u></u><u></u></span></p> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt"><u></u> <u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt">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.<u></u><u></u></span></p> </div> </div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt"><u></u> <u></u></span></p> <div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt">On Fri, 14 Apr 2023 at 19:22, Rajorshi Chattopadhyay <<a href="mailto:rajorshichat@gmail.com" target="_blank">rajorshichat@gmail.com</a>> wrote:<u></u><u></u></span></p> </div> <blockquote style="border-style:none none none solid;border-left-width:1pt;border-left-color:rgb(204,204,204);padding:0cm 0cm 0cm 6pt;margin-left:4.8pt;margin-right:0cm"> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt">Hello all,<u></u><u></u></span></p> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt"><u></u> <u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt">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:<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt"> <u></u><u></u></span></p> </div> <div> <p style="margin-right:0cm;margin-bottom:0cm;margin-left:36pt;font-stretch:normal"> <span style="font-size:8.5pt;font-family:Menlo;color:black">/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':<u></u><u></u></span></p> <p style="margin-right:0cm;margin-bottom:0cm;margin-left:36pt;font-stretch:normal"> <span style="font-size:8.5pt;font-family:Menlo;color:black">libxsmm_malloc.c:(.text.libxsmm_xget_scratch_allocator+0x111): undefined reference to `pthread_yield'<u></u><u></u></span></p> <p style="margin-right:0cm;margin-bottom:0cm;margin-left:36pt;font-stretch:normal"> <span style="font-size:8.5pt;font-family:Menlo;color:black">/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':<u></u><u></u></span></p> <p style="margin-right:0cm;margin-bottom:0cm;margin-left:36pt;font-stretch:normal"> <span style="font-size:8.5pt;font-family:Menlo;color:black">libxsmm_malloc.c:(.text.libxsmm_xrelease_scratch+0x101): undefined reference to `pthread_yield'<u></u><u></u></span></p> <p style="margin-right:0cm;margin-bottom:0cm;margin-left:36pt;font-stretch:normal"> <span style="font-size:8.5pt;font-family:Menlo;color:black">/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<u></u><u></u></span></p> <p style="margin-right:0cm;margin-bottom:0cm;margin-left:36pt;font-stretch:normal"> <span style="font-size:8.5pt;font-family:Menlo;color:black">collect2: error: ld returned 1 exit status<u></u><u></u></span></p> <p style="margin-right:0cm;margin-bottom:0cm;margin-left:36pt;font-stretch:normal"> <span style="font-size:8.5pt;font-family:Menlo;color:black">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<u></u><u></u></span></p> <p style="margin-right:0cm;margin-bottom:0cm;margin-left:36pt;font-stretch:normal"> <span style="font-size:8.5pt;font-family:Menlo;color:black">make[2]: *** [/home/rajorshi/cp2k-9.1/Makefile:158: all] Error 2<u></u><u></u></span></p> <p style="margin-right:0cm;margin-bottom:0cm;margin-left:36pt;font-stretch:normal"> <span style="font-size:8.5pt;font-family:Menlo;color:black">make[1]: *** [/home/rajorshi/cp2k-9.1/Makefile:140: ssmp] Error 2<u></u><u></u></span></p> <p style="margin-right:0cm;margin-bottom:0cm;margin-left:36pt;font-stretch:normal"> <span style="font-size:8.5pt;font-family:Menlo;color:black">make[1]: *** Waiting for unfinished jobs....<u></u><u></u></span></p> <p style="margin-right:0cm;margin-bottom:0cm;margin-left:36pt;font-stretch:normal"> <span style="font-size:8.5pt;font-family:Menlo;color:black">make[2]: *** [/home/rajorshi/cp2k-9.1/Makefile:158: all] Error 2<u></u><u></u></span></p> <p style="margin-right:0cm;margin-bottom:0cm;margin-left:36pt;font-stretch:normal"> <span style="font-size:8.5pt;font-family:Menlo;color:black">make[1]: *** [/home/rajorshi/cp2k-9.1/Makefile:140: sdbg] Error 2<u></u><u></u></span></p> <p style="margin-right:0cm;margin-bottom:0cm;margin-left:36pt;font-stretch:normal"> <span style="font-size:8.5pt;font-family:Menlo;color:black">make: *** [Makefile:135: all] Error 2<u></u><u></u></span></p> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt"><u></u> <u></u></span></p> </div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt">I find that the libxsmm library was installed successfully in the previous step. <u></u><u></u></span></p> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt">I have attached the entire output of make and the arch file for reference. <u></u><u></u></span></p> </div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt">-- <u></u><u></u></span></p> <div> <div> <div> <div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt;font-family:Arial,sans-serif">With Regards,</span><span style="font-size:11pt"><u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt;font-family:Arial,sans-serif">Rajorshi Chattopadhyay,</span><span style="font-size:11pt"><u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt;font-family:Arial,sans-serif">PhD Researcher in Mineralogy/Crystallography,</span><span style="font-size:11pt"><u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt;font-family:Arial,sans-serif">Institut für Geologie und Mineralogie,</span><span style="font-size:11pt"><u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt;font-family:Arial,sans-serif">Universität zu Köln, Germany</span><span style="font-size:11pt"><u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:12pt"><u></u> <u></u></span></p> </div> </div> </div> </div> </div> </div> </div> </blockquote> </div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt"><br clear="all"> <u></u><u></u></span></p> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt"><u></u> <u></u></span></p> </div> <p class="MsoNormal" style="margin-left:36pt"><span class="m_4448274704660630580gmailsignatureprefix"><span style="font-size:11pt">-- </span></span><span style="font-size:11pt"><u></u><u></u></span></p> <div> <div> <div> <div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt;font-family:Arial,sans-serif">With Regards,</span><span style="font-size:11pt"><u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt;font-family:Arial,sans-serif">Rajorshi Chattopadhyay,</span><span style="font-size:11pt"><u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt;font-family:Arial,sans-serif">PhD Researcher in Mineralogy/Crystallography,</span><span style="font-size:11pt"><u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt;font-family:Arial,sans-serif">Institut für Geologie und Mineralogie,</span><span style="font-size:11pt"><u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt;font-family:Arial,sans-serif">Universität zu Köln, Germany</span><span style="font-size:11pt"><u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:12pt"><u></u> <u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:9.5pt"></span><span style="font-size:12pt"><u></u><u></u></span></p> </div> </div> </div> </div> </div> <p class="MsoNormal" style="margin-left:36pt"><span style="font-size:11pt">-- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+unsubscribe@googlegroups.com" target="_blank">cp2k+unsubscribe@googlegroups.com</a>.<br> To view this discussion on the web visit <a 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</div></blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><font face="Arial, sans-serif"><span style="line-height:16.12px">With Regards,</span></font></div><div><font face="Arial, sans-serif">Rajorshi Chattopadhyay,</font></div><div><font face="Arial, sans-serif">PhD Researcher in Mineralogy/Crystallography,</font></div><div><font face="Arial, sans-serif"><span style="line-height:16.12px">Institut für Geologie und Mineralogie,</span></font></div><div><font face="Arial, sans-serif"><span style="line-height:16.12px">Universität zu Köln, Germany<br></span></font></div><div style="font-size:small"><br></div><div style="font-size:small"><span style="line-height:16.12px;font-size:12.8px"></span></div></div></div></div></div> <p></p> -- <br /> You received this message because you are subscribed to the Google Groups "cp2k" group.<br /> To unsubscribe from 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