<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="">Dear Will,<div class=""><br class=""></div><div class="">Thanks so much for your help. Using the virtual environment by anaconda, now I can run the overall test system smoothly, despite some failed tests. </div><div class=""><br class=""><div class="">
<div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="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;">Thank you for considering my request.</div><div style="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;">Sheng-Chih Lin</div><div style="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;"><a href="mailto:r03223130@ntu.edu.tw" class="">r03223130@ntu.edu.tw</a></div><div style="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;" class=""><br class=""></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline">
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<div><br class=""><blockquote type="cite" class=""><div class="">Will DeBenedetti <<a href="mailto:wjd74@cornell.edu" class="">wjd74@cornell.edu</a>> 於 2019年9月22日 下午8:11 寫道：</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class="">Hi Sheng-Chinh,<div class=""><br class=""></div><div class="">I also recall having this error at some point. Usually 99.99% of these errors have to do with PATH variables being incorrectly set. For a number of reasons, I do not use the Python that ships with Macs, I instead use virtual environments using Anaconda (not an endorsement, just a much painless way of using software that Apple will soon deprecate). I was able to get the test suite running by creating a virtual environment using Python 2.7.something and activating this environment using <span style="font-family: Menlo; font-size: 11px;" class=""> </span><font face="Menlo" class=""><span style="font-size:11px" class="">condo</span><span style="font-size:11px" class=""> activate name_of_environment </span></font><span style="font-family: Menlo; font-size: 11px;" class=""> </span></div><div class=""><br class=""></div><div class="">As per the documentation you will to run <span style="font-family: Menlo; font-size: 11px;" class="">make run-tests-foo,</span> then the tests will run serially or in parallel. Keep in mind only PW, CP, PH, and EPW binaries are supported. Make sure you have statically lined these four binaries as per my previous message and verify using otool -L otherwise the tests will crash. I have a 4-core processor and the tests took quite some time running in parallel on the Intel compiler suite. Running on gFortran will be slower.</div><div class=""><br class=""></div><div class="">Will DeBenedetti</div><div class=""><span style="font-family: Menlo; font-size: 11px;" class=""><br class=""></span></div><div class=""><span style="font-family: Menlo; font-size: 11px;" class=""> </span></div></div></div></div></div></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Sep 22, 2019 at 2:03 AM 林聖智 <<a href="mailto:r03223130@ntu.edu.tw" class="">r03223130@ntu.edu.tw</a>> wrote:<br class=""></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 style="word-wrap:break-word;line-break:after-white-space" class="">Hi Will, <div class=""><br class=""></div><div class="">Thanks so much for the info. I’ve checked libraries of pw.x and it seems good for them with static addresses. So, I carried out calculations, such as scf and vc_relax, and they worked smoothly. Thus, I think the absence of messages I mentioned in previous e-mail was caused by some of the bins having dynamic addresses. And it could be fixed by replacing their addresses. </div><div class=""><br class=""></div><div class="">Besides, when I ran test files (make run-tests-pw-serial) in the file--test-suite, the system showed the message below.</div><div class=""><span style="font-family:Menlo;font-size:11px;background-color:rgb(255,255,255)" class=""><br class=""></span></div><div class=""><span style="font-family:Menlo;font-size:11px;background-color:rgb(255,255,255)" class="">env: python2: No such file or directory</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">make: *** [run-tests-pw-serial] Error 127</span></div><div class=""><br class=""></div><div class="">I’ve tried several ways to address it. I checked the installation of python2 and its version was 2.7.16. Besides, I also made a symbolic link to direct the system to the location of python 2.7 using the command as follows, but still no joy. Have you ever experienced the situation?</div><div class=""><br class=""></div><div class=""><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ln -s /opt/local/bin/python2.7 /Users/hayashikiyoshisatoshi/Desktop/q-e-qe-6.4.1/q-e-qe-6.4.1/test-suite/python2</span></div></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div class=""><div class="">
<div dir="auto" style="word-wrap:break-word;line-break:after-white-space" class=""><div style="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;" class="">Thank you for considering my request.</div><div style="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;" class="">Sheng-Chih Lin</div><div style="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;" class=""><a href="mailto:r03223130@ntu.edu.tw" target="_blank" class="">r03223130@ntu.edu.tw</a></div><div style="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;" class=""><br class=""></div><br class="gmail-m_4459915269498802889Apple-interchange-newline"></div><br class="gmail-m_4459915269498802889Apple-interchange-newline">
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<div class=""><br class=""><blockquote type="cite" class=""><div class="">Will DeBenedetti <<a href="mailto:wjd74@cornell.edu" target="_blank" class="">wjd74@cornell.edu</a>> 於 2019年9月22日 上午9:52 寫道：</div><br class="gmail-m_4459915269498802889Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class="">Hi Sheng-Chinh,<div class=""><br class=""></div><div class="">Have you looked to see if you have made QE binaries? These will be in the /qe/bin On my machine these are located here: <span style="font-family:Menlo;font-size:11px" class="">/Users/wjid/qe/bin</span></div><div class=""><br class=""></div><div class="">Using <span style="font-family:Menlo;font-size:11px" class="">ls</span> shows the following after running `make all`:</div><div class=""><br class=""></div><div class=""><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">wjid$ ls</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">alpha2f.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>neb.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">average.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>open_grid.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">band.eps<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>path_interpolation.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">bands.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>ph.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">bse_main.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>phcg.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">cell2ibrav.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>plan_avg.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">cp.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>plotband.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">dist.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>plotproj.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">dos.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>plotrho.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">dynmat.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>pmw.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">epa.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>pp.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">epsilon.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>ppacf.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ev.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>projwfc.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">fd.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>pw.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">fd_ef.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>pw2bgw.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">fd_ifc.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>pw2critic.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">fermi_proj.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>pw2gw.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">fermi_velocity.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>pw2wannier90.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">fqha.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>pw4gww.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">fs.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>pwcond.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">generate_rVV10_kernel_table.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>pwi2xsf.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">generate_vdW_kernel_table.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>q2qstar.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">gww.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>q2r.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">gww_fit.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>q2trans.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">head.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>q2trans_fd.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">hp.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>simple.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ibrav2cell.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>simple_bse.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">initial_state.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>simple_ip.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">iotk<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>spectra_correction.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">iotk.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>sumpdos.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">iotk_print_kinds.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>turbo_davidson.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">kpoints.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>turbo_eels.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">lambda.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>turbo_lanczos.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ld1.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>turbo_spectrum.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">manycp.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>wannier_ham.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">manypw.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>wannier_plot.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">matdyn.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>wfck2r.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">molecularnexafs.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>wfdd.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">molecularpdos.x<span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>xspectra.x</span></div></div><div class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div class="">Then you should verify that your binaries are linked properly by using otool, which is the linux equivalent of ldd. <br class=""></div><div class=""><br class=""></div><div class="">The command to show which shared libraries are linked with this binary use otool -L (in terminal)</div><div class=""><br class=""></div><div class=""><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">wjid$ otool -L pw.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">pw.x:</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_scalapack_lp64.dylib (compatibility version 0.0.0, current version 0.0.0)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_intel_lp64.dylib (compatibility version 0.0.0, current version 0.0.0)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_intel_thread.dylib (compatibility version 0.0.0, current version 0.0.0)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_core.dylib (compatibility version 0.0.0, current version 0.0.0)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_blacs_mpich_lp64.dylib (compatibility version 0.0.0, current version 0.0.0)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.50.4)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>/usr/local/bin/mpich-install/lib/libmpifort.12.dylib (compatibility version 14.0.0, current version 14.7.0)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>/usr/local/bin/mpich-install/lib/libmpi.12.dylib (compatibility version 14.0.0, current version 14.7.0)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>/usr/local/bin/mpich-install/lib/libpmpi.12.dylib (compatibility version 14.0.0, current version 14.7.0)</span></div></div><div class=""><br class=""></div><div class="">The output shows which MKL and mpich libraries are linked to the pw.x binary. </div><div class=""><br class=""></div><div class="">Like I said in my previous email, if you have system integrity protection enabled (it is by default) linking to dynamic libraries is disabled by default. These binaries will look like plotrho.x as below:</div><div class=""><br class=""></div><div class=""><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">wjid$ otool -L plotrho.x</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">plotrho.x:</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>@rpath/libmkl_scalapack_ilp64.dylib (compatibility version 0.0.0, current version 0.0.0)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>@rpath/libmkl_intel_ilp64.dylib (compatibility version 0.0.0, current version 0.0.0)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>@rpath/libmkl_intel_thread.dylib (compatibility version 0.0.0, current version 0.0.0)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>@rpath/libmkl_core.dylib (compatibility version 0.0.0, current version 0.0.0)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>@rpath/libmkl_blacs_mpich_ilp64.dylib (compatibility version 0.0.0, current version 0.0.0)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.50.4)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>/usr/local/bin/mpich-install/lib/libmpifort.12.dylib (compatibility version 14.0.0, current version 14.7.0)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>/usr/local/bin/mpich-install/lib/libmpi.12.dylib (compatibility version 14.0.0, current version 14.7.0)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>/usr/local/bin/mpich-install/lib/libpmpi.12.dylib (compatibility version 14.0.0, current version 14.7.0)</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div></div><div class=""><div class="">To get around this, you can replace the dynamic link with a static address using install_name_tool command as below. For my setup this looks like the following:</div><div class=""><br class=""></div><div class=""> install_name_tool -change "@rpath<span style="font-family:Menlo;font-size:11px" class="">@rpath/libmkl_scalapack_ilp64.</span><span style="font-family:Menlo;font-size:11px" class="">dylib" "</span><span style="font-family:Menlo;font-size:11px" class="">/opt/intel/compilers_and_</span><span style="font-family:Menlo;font-size:11px" class="">libraries_2019.4.233/mac/mkl/</span><span style="font-family:Menlo;font-size:11px" class="">lib/libmkl_scalapack_lp64.</span><span style="font-family:Menlo;font-size:11px" class="">dylib" </Path/To/Binary></span></div></div><div class=""><span style="font-family:Menlo;font-size:11px" class=""><br class=""></span></div><div class=""><div class="">Note that the above command is a one-liner. Repeat this until all of the @rpath/..../ are gone.</div></div><div class=""><br class=""></div><div class="">Will DeBenedetti</div><div class="">Cornell University</div><div class=""><span style="font-family:Menlo;font-size:11px" class=""><br class=""></span></div><div class=""><br class=""></div></div></div></div></div></div></div></div></div></div></div></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Sep 21, 2019 at 9:14 PM 林聖智 <<a href="mailto:r03223130@ntu.edu.tw" target="_blank" class="">r03223130@ntu.edu.tw</a>> wrote:<br class=""></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 style="word-wrap:break-word;line-break:after-white-space" class="">Hi Will,<div class=""><br class=""></div><div class="">Thanks for reaching out to me. But, I am really new to QE and do not understand what files I need to identify. Can you give me more details?</div><div class=""><br class=""></div><div class="">Also, I leave the message, as follows, I got in the end of the ‘'make all'' command. Hope this can help identify the problem.</div><div class=""><br class=""></div><div class=""><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ld: warning: text-based stub file /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory.tbd and library file /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory are out of sync. Falling back to library file for linking.</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ld: warning: text-based stub file /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS.tbd and library file /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS are out of sync. Falling back to library file for linking.</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">( cd ../../bin ; ln -fs ../GWW/bse/bse_main.x . )</span></div></div><div class=""><br class=""></div><div class=""><div class="">
<div dir="auto" style="word-wrap:break-word;line-break:after-white-space" class=""><div style="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" class="">Thank you for considering my request.</div><div style="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" class="">Sheng-Chih Lin</div><div style="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" class=""><a href="mailto:r03223130@ntu.edu.tw" target="_blank" class="">r03223130@ntu.edu.tw</a></div><div style="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" class=""><br class=""></div><br class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-m_369871423699743174gmail-m_5633670984881451858gmail-m_816932597483648566Apple-interchange-newline"></div><br class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-m_369871423699743174gmail-m_5633670984881451858gmail-m_816932597483648566Apple-interchange-newline">
</div>
<div class=""><br class=""><blockquote type="cite" class=""><div class="">Will DeBenedetti <<a href="mailto:wjd74@cornell.edu" target="_blank" class="">wjd74@cornell.edu</a>> 於 2019年9月21日 下午10:28 寫道：</div><br class="gmail-m_4459915269498802889gmail-m_-8405643958124110758gmail-m_369871423699743174gmail-m_5633670984881451858gmail-m_816932597483648566Apple-interchange-newline"><div class=""><span style="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;text-decoration:none;float:none;display:inline" class="">Path/To/QE/Binaries</span></div></blockquote></div><br class=""></div></div>_______________________________________________<br class="">
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer" target="_blank" class="">www.max-centre.eu/quantum-espresso</a>)<br class="">
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_______________________________________________<br class="">Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" target="_blank" class="">www.max-centre.eu/quantum-espresso</a>)<br class="">users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank" class="">users@lists.quantum-espresso.org</a><br class=""><a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank" class="">https://lists.quantum-espresso.org/mailman/listinfo/users</a></div></blockquote></div><br class=""></div></div>_______________________________________________<br class="">
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer" target="_blank" class="">www.max-centre.eu/quantum-espresso</a>)<br class="">
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_______________________________________________<br class="">Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" class="">www.max-centre.eu/quantum-espresso</a>)<br class="">users mailing list <a href="mailto:users@lists.quantum-espresso.org" class="">users@lists.quantum-espresso.org</a><br class=""><a href="https://lists.quantum-espresso.org/mailman/listinfo/users" class="">https://lists.quantum-espresso.org/mailman/listinfo/users</a></div></blockquote></div><br class=""></div></body></html>