<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Asif,<div><br></div><div>Since you're a recent convert to Mac, let me recommend you look into a Mac package manger called Homebrew: <a href="http://mxcl.github.com/homebrew/">http://mxcl.github.com/homebrew/</a>. Homebrew has rules for building OpenMPI, MPICH2, HDF5, and many, many other useful packages. It is really easy to use, just follow what's in the wiki and FAQ pages. </div><div><br></div><div>I recommend Homebrew for anyone that uses a Mac for scientific computing! (double entendre intended)</div><div><br></div><div>Cheers,</div><div>Sean</div><div><br><div apple-content-edited="true">
<span class="Apple-style-span" style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; border-collapse: separate; border-spacing: 0px; -webkit-text-decorations-in-effect: none; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br class="Apple-interchange-newline">--------------------------------------------------------</div><div>Sean M. Couch, Ph.D.</div><div>Hubble Fellow</div><div>Flash Center for Computational Science</div><div>Department of Astronomy & Astrophysics</div><div>The University of Chicago</div><div>5747 S Ellis Ave, Jo 315</div><div>Chicago, IL 60637</div><div>(773) 702-3899</div><div><a href="http://www.flash.uchicago.edu/~smc">www.flash.uchicago.edu/~smc</a></div><div><br></div></div></span></span><br class="Apple-interchange-newline">
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<br><div><div>On Feb 10, 2013, at 7:04 PM, John ZuHone <<a href="mailto:jzuhone@milkyway.gsfc.nasa.gov">jzuhone@milkyway.gsfc.nasa.gov</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Asif,<br><br>Make sure that you don't add the -lgfortran immediately after the -o flag; the compiler will think you intended to link into something else. -o should go last. I'd put the -lgfortran flag in the LIB_OPT variable instead to avoid this. <br><br>I'd also recommend compiling OpenMPI... that's the best way to avoid any possible incompatibilites with the library and your system compilers. <br><br>Let us know what you come up with.<br><br>Best,<br><br>John<br><br>On Feb 10, 2013, at 7:27 PM, Asif ud-Doula <<a href="mailto:auu4@psu.edu">auu4@psu.edu</a>> wrote:<br><br><blockquote type="cite"><br><br>On 2/10/13 6:42 PM, John ZuHone wrote:<br><blockquote type="cite">Asif,<br><br>Does this error come in the linking step at the end? If you haven't already, you might need to add -lgfortran to the link step.<br></blockquote>Yes, it does. I did add -lgfortran to LFLAGS_OPT, but I still got an error, although different one:<br>gfortran: error: flash4: No such file or directory<br>make: *** [flash4] Error 1<br><blockquote type="cite"><br>I was under the impression gfortran did not come with Xcode and needed to be installed from a separate source.<br></blockquote>Now that I think about it, I might have installed separately. I think I had C compiler in mind.<br><br><br>At least that's what I've had to do.<br><blockquote type="cite"><br>Did you compile OpenMPI or install a binary?<br></blockquote>I installed binary.<br><br>Asif<br><br><blockquote type="cite"><br>Best,<br><br>John Z<br><br>John ZuHone<br>Laboratory for High-Energy Astrophysics<br>NASA/Goddard Space Flight Center<br>8800 Greenbelt Rd., Code 662<br>Greenbelt, MD 20771<br>(w) 301-286-2531<br>(m) 773-758-0172<br><a href="mailto:jzuhone@gmail.com">jzuhone@gmail.com</a><br>john.zuhone@nasa.gov<br><br>On Feb 10, 2013, at 6:06 PM, Asif ud-Doula <auu4@psu.edu> wrote:<br><br><blockquote type="cite">Hi,<br>I am attempting to compile the latest version on Mac OS X (Lion), but had some trouble linking when testing with './setup Sedov -auto'. Here is an excerpt from the compilation error:<br><br>Undefined symbols for architecture x86_64:<br> "__gfortran_transfer_character_write", referenced from:<br> _driver_abortflash_ in Driver_abortFlash.o<br> _driver_checkmpierrorcode_ in Driver_checkMPIErrorCode.o<br> _driver_computedt_ in Driver_computeDt.o<br> _driver_evolveflash_ in Driver_evolveFlash.o<br> _driver_initflash_ in Driver_initFlash.o<br> _driver_verifyinitdt_ in Driver_verifyInitDt.o<br> _eos_ in Eos.o<br> ...<br>ld: symbol(s) not found for architecture x86_64<br>collect2: ld returned 1 exit status<br>make: *** [flash4] Error 1<br><br><br>'uname -a' produces: 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64<br><br>I am new MAc user, so I could easily be making a basic mistake. However, I am using Xcode that comes with gfortran. I also installed the latest stable version of OpenMPI.<br><br>Any suggestion will be welcome. Thanks in advance for your time,<br>Asif<br><br><br>-<br></blockquote><br><br></blockquote></blockquote></blockquote></div><br></div></body></html>