<div dir="ltr">Hello,<div><br></div><div>Where can I find those precompiled binaries? Also, for the external software packages, I would like to have a look at that script that you have.</div><div><br></div><div>Thanks,</div><div><br></div><div>David</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, May 29, 2015 at 11:40 AM, Mary Haley <span dir="ltr"><<a href="mailto:haley@ucar.edu" target="_blank">haley@ucar.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-size:small">Hi David,</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">First, though, would you be able to use one of our precompiled NCL binaries for LINUX, so you don't have to do the build yourself? We have Debian and RedHat binaries, and you should be able to use these on other flavors of Linux.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">If you still want to do the source build yourself, then here are the env vars I recommend setting:</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><div class="gmail_default">export CC=gcc</div><div class="gmail_default">export CXX=g++</div><div class="gmail_default">export FC=gfortran</div><div class="gmail_default">export F77=gfortran</div><div class="gmail_default">export F90=gfortran</div><div class="gmail_default"><br></div><div class="gmail_default">Using "f77" (lowercase) is probably not going to affect anything on your system.</div><div class="gmail_default"><br></div><div class="gmail_default">You may also want:</div><div class="gmail_default"><br></div><div class="gmail_default"><div class="gmail_default">export CFLAGS=-fPIC</div><div class="gmail_default">export FFLAGS=-fPIC</div><div class="gmail_default">export F90FLAGS=-fPIC</div><div class="gmail_default">export CXXFLAGS=-fPIC</div><div class="gmail_default"><br></div><div class="gmail_default">This is your chance to set any other particular flags you want, like optimization flags. I usually try to keep it as "bare" as possible and let the compiler figure out the options it wants to use.</div><div class="gmail_default"><br></div><div class="gmail_default">Finally, as a precaution, I recommend setting LINUX_BRAND, depending on whether you have a 32-bit or 64-bit system:</div><div class="gmail_default"><br></div><div class="gmail_default">
<p><span>export</span> LINUX_BRAND linux64</p><p><span>or</span></p><p><span>export</span> LINUX_BRAND linux32</p><p>If you are having to do a full blown build of all those external software packages that NCL depends on, let me know. I have a script that can help with this. </p><span class="HOEnZb"><font color="#888888"><p>--Mary</p><p><br></p><div><br></div></font></span></div></div></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Fri, May 29, 2015 at 11:22 AM, David Stanfel <span dir="ltr"><<a href="mailto:dstanfel@ualberta.ca" target="_blank">dstanfel@ualberta.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello,<div><br></div><div>Thanks for the reply. I would like to try that. How would I go about specifying the use of gcc and gfortran? I set the environment variables:</div><div><br></div><div>export CC=gcc</div><div>export f77=gfortran</div><div><br></div><div>What more would be needed?</div><div><br></div><div>Thanks,</div><div><br></div><div>David</div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, May 29, 2015 at 11:05 AM, Mary Haley <span dir="ltr"><<a href="mailto:haley@ucar.edu" target="_blank">haley@ucar.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-size:small">[Before I address this issue, I would like to appeal to other people subscribed to ncl-install to see if anybody has successfully built NCL using the "clang" compiler on MacOS, paired with a fortran compiler like "gfortran".]</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">Hi David,</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">The config.log file was very helpful, thanks.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">I hate to deflect this, but this looks like an issue that perhaps the HDF-EOS5 people need to address.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">The problem is that "h5cc" is being used build HDF-EOS5, which is what it should do, but apparently HDF5 was built with "clang", so this got put into "h5cc", and HDF-EOS5 doesn't seem to work with "clang". Here's the place in the "config.log" file that I think is the source of the problem:</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default"><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">configure:22754: checking for hdf5 szip encoding filter</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">configure:22796: /usr/local/hdf5-1.8.15/bin/h5cc -o conftest -g -O2 -I/usr/local/hdf5-1.8.15</font><font face="monospace, monospace">//include -I/usr/local/zlib-1.2.8//include -I/usr/local/szip-2.1//include -I/usr/local/hdf5</font><font face="monospace, monospace">-1.8.15//include -L/usr/local/zlib-1.2.8//lib -L/usr/local/szip-2.1//lib -L/usr/local/hdf5-</font><span style="font-family:monospace,monospace">1.8.15//lib conftest.c -lhdf5_hl -lhdf5 -lsz -lz -lm >&5</span></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">clang: warning: argument unused during compilation: '-L/usr/local/zlib-1.2.8//lib'</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">clang: warning: argument unused during compilation: '-L/usr/local/szip-2.1//lib'</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">clang: warning: argument unused during compilation: '-L/usr/local/hdf5-1.8.15//lib'</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">conftest.c:41:21: warning: implicitly declaring library function 'exit' with type 'void (int</font><span style="font-family:monospace,monospace">) __attribute__((noreturn))'</span></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace"> if (ret < 0) exit(1);</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace"> ^</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">conftest.c:41:21: note: please include the header <stdlib.h> or explicitly provide a declara</font><span style="font-family:monospace,monospace">tion for 'exit'</span></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">1 warning generated.</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">configure:22799: $? = 0</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">configure:22805: ./conftest</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace">HDF5-DIAG: Error detected in HDF5 (1.8.15) thread 0:</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace"> #000: H5Z.c line 1673 in H5Zget_filter_info(): Filter info not retrieved</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace"> major: Data filters</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace"> minor: Can't get value</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace"> #001: H5Z.c line 1703 in H5Z_get_filter_info(): Filter not defined</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace"> major: Data filters</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace"> minor: Bad value</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace"> #002: H5Z.c line 1247 in H5Z_find(): required filter is not registered</font></div><div class="gmail_default" style="font-size:small"><font face="monospace, monospace"> major: Data filters</font></div><div><div><font face="monospace, monospace"> minor: Object not found</font></div><div><font face="monospace, monospace">configure:22808: $? = 1</font></div><div><font face="monospace, monospace">configure: program exited with status 1</font></div></div></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">My general recommendation, as a work-around for now, is to try to build things with gcc/gfortran, and not clang. This means you would need to rebuild HDF5, and potentially szip and zlib with gcc/gfortran.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">Or, you can appeal to the HDF-EOS5 folks to see if they know how to get this library built with clang.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">I hope to attempt a clang build soon, which I believe will have to be paired with gfortran because Apple hasn't provided a native Fortran compiler that I know of. Clang is supposed to work interchangeably with gcc, but I haven't had a chance to verify this.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">Let me know if you want to try the gcc/gfortran build solution, but are not sure where to start.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">--Mary</div><div class="gmail_default" style="font-size:small"><br></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Thu, May 28, 2015 at 3:02 PM, David Stanfel <span dir="ltr"><<a href="mailto:dstanfel@ualberta.ca" target="_blank">dstanfel@ualberta.ca</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><span style="font-size:13px">Hello,</span><div style="font-size:13px"><br></div><div style="font-size:13px">I am trying to make the HDF-EOS5 software on my Macbook Pro (OS X 10.9.5) to build and install NCL but I am having some issues. </div><div style="font-size:13px"><br></div><div style="font-size:13px">I tried to use the 'make all install' command but that produced:</div><div style="font-size:13px"><br></div><div style="font-size:13px"><p style="margin:0px;font-size:11px;font-family:Menlo">make: *** No rule to make target `all'. Stop.</p><p style="margin:0px;font-size:11px;font-family:Menlo"><br></p></div><div style="font-size:13px">When trying to run the 'make' command: </div><div style="font-size:13px"><br></div><div style="font-size:13px"><p style="margin:0px;font-size:11px;font-family:Menlo">dstanfel:hdfeos5 ninjawarrior343$ make</p><p style="margin:0px;font-size:11px;font-family:Menlo">This file is for use by ECS Configuration Management processes only.</p><p style="margin:0px;font-size:11px;font-family:Menlo"><br></p><p style="margin:0px"><font face="arial, helvetica, sans-serif"> I have attached the config.log in case it is of some use.</font></p><p style="margin:0px"><font face="arial, helvetica, sans-serif"><br></font></p><p style="margin:0px"><font face="arial, helvetica, sans-serif">Thanks,</font></p><p style="margin:0px"><font face="arial, helvetica, sans-serif"><br></font></p><p style="margin:0px"><font face="arial, helvetica, sans-serif">David </font></p></div></div>
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