<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> <meta name="Generator" content="Microsoft Word 15 (filtered medium)"> <style></style> </head> <body lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"> <div class="WordSection1"> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt;mso-fareast-language:EN-US">Hi<o:p></o:p></span></p> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Did you try to add the linker flag “-lpthread”.<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">HTH<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Matthias<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> <b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">cp2k@googlegroups.com <cp2k@googlegroups.com> on behalf of Rajorshi Chattopadhyay <rajorshichat@gmail.com><br> <b>Date: </b>Saturday, 15 April 2023 at 01:07<br> <b>To: </b>cp2k@googlegroups.com <cp2k@googlegroups.com><br> <b>Subject: </b>[CP2K:18667] Re: Error in compiling Cp2k with PLUMED<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Hello all,<o:p></o:p></span></p> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">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.<o:p></o:p></span></p> </div> </div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> <div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">On Fri, 14 Apr 2023 at 19:22, Rajorshi Chattopadhyay <<a href="mailto:rajorshichat@gmail.com">rajorshichat@gmail.com</a>> wrote:<o:p></o:p></span></p> </div> <blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Hello all,<o:p></o:p></span></p> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">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:<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"> <o:p></o:p></span></p> </div> <div> <p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;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':<o:p></o:p></span></p> <p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;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'<o:p></o:p></span></p> <p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;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':<o:p></o:p></span></p> <p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;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'<o:p></o:p></span></p> <p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;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<o:p></o:p></span></p> <p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;font-stretch:normal"> <span style="font-size:8.5pt;font-family:Menlo;color:black">collect2: error: ld returned 1 exit status<o:p></o:p></span></p> <p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;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<o:p></o:p></span></p> <p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;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<o:p></o:p></span></p> <p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;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<o:p></o:p></span></p> <p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;font-stretch:normal"> <span style="font-size:8.5pt;font-family:Menlo;color:black">make[1]: *** Waiting for unfinished jobs....<o:p></o:p></span></p> <p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;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<o:p></o:p></span></p> <p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;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<o:p></o:p></span></p> <p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;font-stretch:normal"> <span style="font-size:8.5pt;font-family:Menlo;color:black">make: *** [Makefile:135: all] Error 2<o:p></o:p></span></p> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> </div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">I find that the libxsmm library was installed successfully in the previous step. <o:p></o:p></span></p> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">I have attached the entire output of make and the arch file for reference. <o:p></o:p></span></p> </div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">-- <o:p></o:p></span></p> <div> <div> <div> <div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Arial",sans-serif">With Regards,</span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Arial",sans-serif">Rajorshi Chattopadhyay,</span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Arial",sans-serif">PhD Researcher in Mineralogy/Crystallography,</span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Arial",sans-serif">Institut für Geologie und Mineralogie,</span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Arial",sans-serif">Universität zu Köln, Germany</span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:12.0pt"><o:p> </o:p></span></p> </div> </div> </div> </div> </div> </div> </div> </blockquote> </div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><br clear="all"> <o:p></o:p></span></p> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> </div> <p class="MsoNormal" style="margin-left:36.0pt"><span class="gmailsignatureprefix"><span style="font-size:11.0pt">-- </span></span><span style="font-size:11.0pt"><o:p></o:p></span></p> <div> <div> <div> <div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Arial",sans-serif">With Regards,</span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Arial",sans-serif">Rajorshi Chattopadhyay,</span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Arial",sans-serif">PhD Researcher in Mineralogy/Crystallography,</span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Arial",sans-serif">Institut für Geologie und Mineralogie,</span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Arial",sans-serif">Universität zu Köln, Germany</span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:12.0pt"><o:p> </o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.5pt"></span><span style="font-size:12.0pt"><o:p></o:p></span></p> </div> </div> </div> </div> </div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">-- <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">cp2k+unsubscribe@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/CACTJSRcWQSW-ZCHy2bcZ9Yg%2B57fo0tVJ8jxXwLc%2BF8u3JEjUiA%40mail.gmail.com?utm_medium=email&utm_source=footer"> https://groups.google.com/d/msgid/cp2k/CACTJSRcWQSW-ZCHy2bcZ9Yg%2B57fo0tVJ8jxXwLc%2BF8u3JEjUiA%40mail.gmail.com</a>.<o:p></o:p></span></p> </div> </body> </html> <p></p> -- <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">cp2k+unsubscribe@googlegroups.com</a>.<br /> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/ZRAP278MB0827DC0DCDBE58EEB5D598E9F49E9%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/ZRAP278MB0827DC0DCDBE58EEB5D598E9F49E9%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM</a>.<br />