<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 Klaus and the others who helped me,<div class=""><br class=""></div><div class="">I found the solution to the last problem: it was due to an error in the LD_LIBRARY_PATH in my ~/.profile file.</div><div class="">Since I was appending to the LD_LIBRARY_PATH the path to a serial hdf5 build, the linker was looking in the wrong path, because the good one was not written correctly. When I deleted the non-parallel path, the linker was not able to find the hdf5 library at all, and I was able to understand the mistake.</div><div class="">The make process for FLASH instead was successful because the path to the hdf5 library was correct in the Makefile.h.</div><div class="">This made the debug tricky.</div><div class=""><br class=""></div><div class="">Thank you again, </div><div class="">Best</div><div class="">Mattia<br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div class=""><br class="Apple-interchange-newline">························································</div> Dr <b class="">Mattia Cipriani,</b> PhD<br class=""> FSN-FUSPHY-SAD<br class=""> ENEA Centro Ricerche Frascati<br class=""><div class=""> 45, Via E. Fermi<br class=""> 00044 Frascati (Rome)<br class=""> Italy</div><div class=""> Ufficio: Edificio 12<div style="line-height: normal;" class=""> Stanza 12029</div> Tel. +39 069400 5145 <br class=""> mobile +39 328 5552077<br class="">························································</div></div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class=""></div></div></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
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<div><br class=""><blockquote type="cite" class=""><div class="">Il giorno 11 mar 2019, alle ore 20:51, Mattia Cipriani <<a href="mailto:mattia.cipriani@enea.it" class="">mattia.cipriani@enea.it</a>> ha scritto:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="content-type" content="text/html; charset=utf-8" class=""><div dir="auto" class="">Dear Klaus,<div class=""><br class=""></div><div class="">Yes, it is surprising because the hdf5 library has been built in parallel and also the tests made using make check were all good.</div><div class="">I understand the difficulty of debugging remotely, I really appreciated your help.</div><div class="">I will try by myself to understand if the problem is related to the system configuration. Since I am running flash on a cluster it might be the case.</div><div class=""><br class=""></div><div class="">Best regards,</div><div class="">Mattia<br class=""><br class=""><div dir="ltr" class=""><div class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">························································</span></div><span style="background-color: rgba(255, 255, 255, 0);" class=""> Dr <b class="">Mattia Cipriani,</b> PhD<br class=""> FSN-FUSPHY-SAD<br class=""> ENEA Centro Ricerche Frascati<br class=""></span><div class=""><span style="background-color: rgba(255, 255, 255, 0);" class=""> <a href="x-apple-data-detectors://2" dir="ltr" x-apple-data-detectors="true" x-apple-data-detectors-type="address" x-apple-data-detectors-result="2" style="-webkit-text-decoration-color: rgba(0, 0, 0, 0.258824);" class="">45, Via E. Fermi</a><br class=""><a href="x-apple-data-detectors://2" dir="ltr" x-apple-data-detectors="true" x-apple-data-detectors-type="address" x-apple-data-detectors-result="2" style="-webkit-text-decoration-color: rgba(0, 0, 0, 0.258824);" class=""> 00044</a> Frascati (Rome)<br class=""> Italy</span></div><div class=""><span style="background-color: rgba(255, 255, 255, 0);" class=""> Ufficio: Edificio 12</span><div class="" style="line-height: normal;"><span style="background-color: rgba(255, 255, 255, 0);" class=""> Stanza 12029</span></div><span style="background-color: rgba(255, 255, 255, 0);" class=""> Tel. <a href="tel:+39%20069400%205145" dir="ltr" x-apple-data-detectors="true" x-apple-data-detectors-type="telephone" x-apple-data-detectors-result="3" class="">+39 069400 5145</a> <br class=""> mobile <a href="tel:+39%20328%205552077" dir="ltr" x-apple-data-detectors="true" x-apple-data-detectors-type="telephone" x-apple-data-detectors-result="4" class="">+39 328 5552077</a><br class="">························································</span></div></div><div dir="ltr" class=""><br class="">Il giorno 11 mar 2019, alle ore 17:58, Klaus Weide <<a href="mailto:klaus@flash.uchicago.edu" class="">klaus@flash.uchicago.edu</a>> ha scritto:<br class=""><br class=""></div><blockquote type="cite" class=""><div dir="ltr" class=""><span class="">On Sat, 9 Mar 2019, Mattia Cipriani wrote:</span><br class=""><span class=""></span><br class=""><blockquote type="cite" class=""><span class="">Dear Klaus,</span><br class=""></blockquote><blockquote type="cite" class=""><span class=""></span><br class=""></blockquote><blockquote type="cite" class=""><span class="">thank you very much for the patch, which allowed to reach the end of the compilation.</span><br class=""></blockquote><blockquote type="cite" class=""><span class="">However now, when I run the code, I get the following error, at the moment of outputting the first hdf5 file:</span><br class=""></blockquote><blockquote type="cite" class=""><span class="">flash4: symbol lookup error: flash4: undefined symbol: H5Pset_fapl_mpio</span><br class=""></blockquote><span class=""></span><br class=""><span class="">I think this indicates that the HDF5 library with which you have linked </span><br class=""><span class="">FLASH has not been built with parallel support - although it is surprising </span><br class=""><span class="">that you did not already get an error at link time (i.e., in the last </span><br class=""><span class="">stage of running 'make').</span><br class=""><span class=""></span><br class=""><span class="">There may be additional sources of problems if you are running flash4 in a </span><br class=""><span class="">different environment from that in which it was built - in particular, if </span><br class=""><span class="">you are running under a batch system - relating to locations of </span><br class=""><span class="">dynamically linked libraries, LD_LIBRARY_PATH, etc.</span><br class=""><span class=""></span><br class=""><span class="">This is hard to impossible to diagnose remotely without access to the </span><br class=""><span class="">system.</span><br class=""><span class=""></span><br class=""><span class="">Klaus</span><br class=""></div></blockquote></div></div></div></blockquote></div><br class=""></div></body></html>