<html> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> </head> <body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""> Matthias: Adding —lplumed to LIBS worked, thank you. <div class=""><br class=""> </div> <div class="">I had previously tried putting an explicit path in LIBS, i.e., </div> <div class=""> <div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">-L/storage/home/stm9/group/SOFTWARE/plumed-2.8.2/exe/lib</div> <div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><br class=""> </div> <div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">which did not work.</div> <div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><br class=""> </div> <div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Note that the instructions on the CP2K HOWTO webpage <a href="https://www.cp2k.org/howto:install_with_plumed" class="">https://www.cp2k.org/howto:install_with_plumed</a></div> <div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">make no mention of adding —lplumed to LIBS, </div> <div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">and indeed make no mention of —with-plumed being a toolchain option</div> <div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">(which I only discovered by browsing in install_cp2k_toolchain.sh, </div> <div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">after your email implied that PLUMED could be installed via toolchain).</div> <div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">It would be helpful if the instructions on the HOWTO page were clarified.</div> <div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><br class=""> </div> <div class=""> <div>Scott Milner<br class=""> William H. Joyce Professor<br class=""> The Pennsylvania State University<br class=""> Department of Chemical Engineering<br class=""> 204 CBE Building<br class=""> University Park, PA 16802<br class=""> (814) 863-9355<br class=""> <a href="mailto:stm9@psu.edu" class="">stm9@psu.edu</a></div> </div> <div><br class=""> <blockquote type="cite" class=""> <div class="">On May 25, 2023, at 4:46 AM, Krack Matthias <<a href="mailto:matthias.krack@psi.ch" class="">matthias.krack@psi.ch</a>> wrote:</div> <br class="Apple-interchange-newline"> <div class=""> <div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"> <div style="margin: 0cm; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span lang="EN-US" style="font-size: 11pt;" class="">Did you add also<span class="Apple-converted-space"> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Consolas;" class="">“-lplumed</span><span lang="EN-US" style="font-size: 11pt;" class="">” to<span class="Apple-converted-space"> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Consolas;" class="">LIBS</span><span lang="EN-US" style="font-size: 11pt;" class="">?<o:p class=""></o:p></span></div> <div style="margin: 0cm; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span lang="EN-US" style="font-size: 11pt;" class="">The toolchain adds<span class="Apple-converted-space"> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Consolas;" class="">PLUMED_LIBS=”-lplumed -ldl -lstdc++ -lz -ldl”</span><span lang="EN-US" style="font-size: 11pt;" class=""><span class="Apple-converted-space"> </span>to<span class="Apple-converted-space"> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Consolas;" class="">LIBS</span><span lang="EN-US" style="font-size: 11pt;" class="">.<o:p class=""></o:p></span></div> <div style="margin: 0cm; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span lang="EN-US" style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div> <div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0cm 0cm;" class=""> <p class="MsoNormal" style="margin: 0cm 0cm 12pt 36pt; font-size: 10pt; font-family: Calibri, sans-serif;"> <b class=""><span style="font-size: 12pt;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class=""><a href="mailto:cp2k@googlegroups.com" style="color: blue; text-decoration: underline;" class="">cp2k@googlegroups.com</a><span class="Apple-converted-space"> </span><<a href="mailto:cp2k@googlegroups.com" style="color: blue; text-decoration: underline;" class="">cp2k@googlegroups.com</a>> on behalf of Scott Milner <<a href="mailto:stm9@psu.edu" style="color: blue; text-decoration: underline;" class="">stm9@psu.edu</a>><br class=""> <b class="">Date:<span class="Apple-converted-space"> </span></b>Thursday, 25 May 2023 at 02:09<br class=""> <b class="">To:<span class="Apple-converted-space"> </span></b>cp2k <<a href="mailto:cp2k@googlegroups.com" style="color: blue; text-decoration: underline;" class="">cp2k@googlegroups.com</a>><br class=""> <b class="">Subject:<span class="Apple-converted-space"> </span></b>[CP2K:18847] Problems with CP2K+PLUMED build<o:p class=""></o:p></span></p> </div> <div style="margin: 0cm 0cm 0cm 36pt; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 11pt;" class="">After successfully building local.psmp architecture of CP2K, I tried to install CP2K+PLUMED. This failed, as I describe below.<o:p class=""></o:p></span></div> <div class=""> <div class=""> <div style="margin: 0cm 0cm 0cm 36pt; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div> </div> <div class=""> <div style="margin: 0cm 0cm 0cm 36pt; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 11pt;" class="">1) I built PLUMED from source without errors, using the standard procedure:<br class=""> <br class=""> ./configure --prefix=/storage/home/stm9/group/SOFTWARE/plumed-2.8.2/exe<br class=""> make<br class=""> make install<br class=""> <br class=""> 2) I created an architecture file local_PLUMED.psmp file by modifying local.psmp, with these changes , following the instructions on the<span class="Apple-converted-space"> </span><a href="http://cp2k.org/" style="color: blue; text-decoration: underline;" class="">cp2k.org</a><span class="Apple-converted-space"> </span>website<o:p class=""></o:p></span></div> <div class=""> <div style="margin: 0cm 0cm 0cm 36pt; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 11pt;" class="">( <a href="https://www.cp2k.org/howto:install_with_plumed" style="color: blue; text-decoration: underline;" class="">https://www.cp2k.org/howto:install_with_plumed</a>):<o:p class=""></o:p></span></div> </div> <div style="margin: 0cm 0cm 0cm 36pt; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 11pt;" class=""><br class=""> a) lines added at the top<br class=""> <br class=""> include /storage/home/stm9/group/SOFTWARE/plumed-2.8.2/exe/lib/plumed/src/lib/Plumed.inc<br class=""> EXTERNAL_OBJECTS=$(PLUMED_STATIC_DEPENDENCIES)<br class=""> <br class=""> b) added -D__PLUMED2 to DFLAGS<o:p class=""></o:p></span></div> </div> <div class=""> <div style="margin: 0cm 0cm 0cm 36pt; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div> </div> <div class=""> <p class="MsoNormal" style="margin: 0cm 0cm 12pt 36pt; font-size: 10pt; font-family: Calibri, sans-serif;"> <span style="font-size: 11pt;" class="">c) added -lz -ldl -lstdc++ to LIBS<o:p class=""></o:p></span></p> </div> <div class=""> <div style="margin: 0cm 0cm 0cm 36pt; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 11pt;" class="">d) I am not using OPENMPI, so I did not add -lmpi_cxx -lrt to LIBS<o:p class=""></o:p></span></div> </div> <div class=""> <div style="margin: 0cm 0cm 0cm 36pt; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 11pt;" class=""><br class=""> 3) Then the make command<o:p class=""></o:p></span></div> </div> <div class=""> <div style="margin: 0cm 0cm 0cm 36pt; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div> </div> <div class=""> <div style="margin: 0cm 0cm 0cm 36pt; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 11pt;" class=""> make ARCH=local_PLUMED VERSION=psmp<br class=""> <br class=""> fails, with errors in which components of PLUMED are not found:<br class=""> <br class=""> /storage/group/stm9/default/SOFTWARE/cp2k-2023.1-intel/lib/local_PLUMED/psmp/libcp2kmain.a(metadynamics.o): In function `metadynamics_mp_metadyn_finalise_plumed_':<br class=""> /storage/group/stm9/default/SOFTWARE/cp2k-2023.1-intel/src/metadynamics.F:208: undefined reference to `plumed_gfinalize'<br class=""> /storage/group/stm9/default/SOFTWARE/cp2k-2023.1-intel/lib/local_PLUMED/psmp/libcp2kmain.a(metadynamics.o): In function `metadynamics_mp_metadyn_integrator_':<br class=""> /storage/group/stm9/default/SOFTWARE/cp2k-2023.1-intel/src/metadynamics.F:299: undefined reference to `plumed_gcmd'<br class=""> /storage/group/stm9/default/SOFTWARE/cp2k-2023.1-intel/src/metadynamics.F:300: undefined reference to `plumed_gcmd'<br class=""> /storage/group/stm9/default/SOFTWARE/cp2k-2023.1-intel/src/metadynamics.F:301: undefined reference to `plumed_gcmd'<br class=""> /storage/group/stm9/default/SOFTWARE/cp2k-2023.1-intel/src/metadynamics.F:302: undefined reference to `plumed_gcmd'<br class=""> /storage/group/stm9/default/SOFTWARE/cp2k-2023.1-intel/src/metadynamics.F:303: undefined reference to `plumed_gcmd'<br class=""> /storage/group/stm9/default/SOFTWARE/cp2k-2023.1-intel/lib/local_PLUMED/psmp/libcp2kmain.a(metadynamics.o):/storage/group/stm9/default/SOFTWARE/cp2k-2023.1-intel/src/metadynamics.F:304: more undefined references to `plumed_gcmd' follow<br class=""> <br class=""> But the directory<o:p class=""></o:p></span></div> </div> <div class=""> <div style="margin: 0cm 0cm 0cm 36pt; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 11pt;" class="">/storage/home/stm9/group/SOFTWARE/plumed-2.8.2/exe/lib/plumed/src/lib/<o:p class=""></o:p></span></div> </div> <div class=""> <div style="margin: 0cm 0cm 0cm 36pt; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 11pt;" class="">does contain Plumed.inc, with the following contents:<o:p class=""></o:p></span></div> </div> <div class=""> <div style="margin: 0cm 0cm 0cm 36pt; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 11pt;" class=""><br class=""> PLUMED_RUNTIME_LOAD= "/storage/home/stm9/group/SOFTWARE/plumed-2.8.2/exe/lib/libplumedWrapper.a" -ldl<br class=""> PLUMED_STATIC_LOAD= "/storage/home/stm9/group/SOFTWARE/plumed-2.8.2/exe/lib/libplumed.a" -ldl -lstdc++ -lz -ldl -rdynamic -Wl,-Bsymbolic -fopenmp<br class=""> PLUMED_SHARED_LOAD= "/storage/home/stm9/group/SOFTWARE/plumed-2.8.2/exe/lib/libplumed.so" -ldl<br class=""> PLUMED_RUNTIME_DEPENDENCIES=<br class=""> PLUMED_STATIC_DEPENDENCIES= "/storage/home/stm9/group/SOFTWARE/plumed-2.8.2/exe/lib/libplumed.a"<br class=""> PLUMED_SHARED_DEPENDENCIES= "/storage/home/stm9/group/SOFTWARE/plumed-2.8.2/exe/lib/libplumed.so"<br class=""> PLUMED_FORTRAN= "/storage/home/stm9/group/SOFTWARE/plumed-2.8.2/exe/lib/plumed/fortran/plumed.f90"<br class=""> PLUMED_FORTRAN08= "/storage/home/stm9/group/SOFTWARE/plumed-2.8.2/exe/lib/plumed/fortran/plumed_f08.f90"<br class=""> <br class=""> And the directory <br class=""> /storage/home/stm9/group/SOFTWARE/plumed-2.8.2/exe/lib <o:p class=""></o:p></span></div> </div> <div class=""> <div style="margin: 0cm 0cm 0cm 36pt; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 11pt;" class="">does contain the library libplumed.a;<br class=""> and libplumed.a does contain the object PlumedStatic.o;<br class=""> and PlumedStatic.o does contain the missing items:<br class=""> <br class=""> (base) [stm9@submit03 lib]$ nm PlumedStatic.o | grep plumed_gcmd<br class=""> 0000000000000eb0 T plumed_gcmd<br class=""> 0000000000000ed0 T plumed_gcmd_safe<br class=""> (base) [stm9@submit03 lib]$ nm PlumedStatic.o | grep plumed_gfinalize<br class=""> 0000000000000ee0 T plumed_gfinalize<br class=""> <br class=""> I have tried modifying local_PLUMED.psmp, by<br class=""> adding -L/storage/home/stm9/group/SOFTWARE/plumed-2.8.2/exe/lib to LIBS;<br class=""> adding -I/storage/home/stm9/group/SOFTWARE/plumed-2.8.2/exe/include to CFLAGS and FCFLAGS;<o:p class=""></o:p></span></div> </div> <div class=""> <div style="margin: 0cm 0cm 0cm 36pt; font-size: 10pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 11pt;" class="">and adding -L/storage/home/stm9/group/SOFTWARE/plumed-2.8.2/exe/lib to LDFLAGS;<br class=""> with exactly the same errors resulting.<o:p class=""></o:p></span></div> </div> </div> <div class=""> <div style="margin: 0cm 0cm 0cm 36pt; 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