<div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">2015-06-02 17:51 GMT+02:00 Rob Latham <span dir="ltr"><<a href="mailto:robl@mcs.anl.gov" target="_blank">robl@mcs.anl.gov</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class=""><br>
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On 06/02/2015 10:18 AM, Wei-keng Liao wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi, Nick<br>
<br>
I found a Xeon machine that has icc and built 1.6.0 without errors.<br>
icc version 15.0.2 (gcc version 4.4.7 compatibility)<br>
<br>
I also notice from your config.log that CFLAGS was set even you did not set it at configure command line. If you search keyword for "ac_cv_env_CFLAGS_value", you can see it contains compile options<br>
"-m64 -fPIC -O2 -xHost -prec-div ... " See lines 72 and 3419. In my case, that variable is empty.<br>
Something strange in configure triggers the setting of use these explicit compile options.<br>
Maybe you should regenerate file configure by running command "autoreconf".<br>
<br>
The option -fPIC is for building share libraries, which I suspect is the cause of error you are seeing. I built my OpenMPI 1.8.5 with configure option "--enable-static --disable-shared".<br>
I was seeing problems when I used an OpenMPI with shared library option enabled to build netCDF or HDF5, so I disable it. (I remember shared option is discouraged by parallel HDF5.)<br>
Do you know how your OpenMPI was built?<br>
</blockquote>
<br></span>
The shared option was indeed discouraged by HDF5, but linkers have gotten better and systems are no longer (typically) a hodge-podge of random workstations.<br>
<br>
-fPIC is needed if you want to link with Unidata NetCDF, right? Or one can explicitly select and build that whole stack entirely with static libraries. Must make for some large executable files! :></blockquote><div>Yes, I was linking through shared libraries all the way, and actually I have never had problems. </div><div>I guess better safe than sorry...</div><div><br></div><div>And yes, I wanted to reduce the footprint of the installation as it already was at 9gb for installations using as many shared libraries as I could. :( </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="HOEnZb"><font color="#888888"><br>
<br>
==rob</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
Wei-keng<br>
<br>
On Jun 2, 2015, at 9:29 AM, Nick Papior Andersen wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
2015-06-02 16:25 GMT+02:00 Rob Latham <<a href="mailto:robl@mcs.anl.gov" target="_blank">robl@mcs.anl.gov</a>>:<br>
<br>
<br>
On 06/02/2015 02:58 AM, Nick Papior Andersen wrote:<br>
./nctst ./<a href="http://testfile.nc" target="_blank">testfile.nc</a> <<a href="http://testfile.nc" target="_blank">http://testfile.nc</a>><br>
ncmpi_inq_typeids not implemented<br>
[n-62-12-2:21767] *** Process received signal ***<br>
[n-62-12-2:21767] Signal: Segmentation fault (11)<br>
[n-62-12-2:21767] Signal code: Address not mapped (1)<br>
[n-62-12-2:21767] Failing at address: 0xffffffffffffffe8<br>
[n-62-12-2:21767] [ 0] /lib64/libpthread.so.0(+0xf710)[0x2b3e93945710]<br>
[n-62-12-2:21767] [ 1]<br>
/zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(_ZNSo6sentryC2ERSo+0x19)[0x2b3e934ace79]<br>
[n-62-12-2:21767] [ 2]<br>
/zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(_ZSt16__ostream_insertIcSt11char_traitsIcEERSt13basic_ostreamIT_T0_ES6_PKS3_l+0x29)[0x2b3e934ad589]<br>
[n-62-12-2:21767] [ 3]<br>
/zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(_ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_PKc+0x27)[0x2b3e934ad9e7]<br>
[n-62-12-2:21767] [ 4] ./nctst[0x40ad62]<br>
[n-62-12-2:21767] [ 5] ./nctst[0x40b93c]<br>
[n-62-12-2:21767] [ 6]<br>
/lib64/libc.so.6(__libc_start_main+0xfd)[0x2b3e93d76d5d]<br>
[n-62-12-2:21767] [ 7] ./nctst[0x405899]<br>
[n-62-12-2:21767] *** End of error message ***<br>
<br>
I understand the oddity here is that inq_typids is getting called somehow, and so the backtrace is in some ways irrelevant. I ran it through c++filt anyway:<br>
I agree completely.<br>
<br>
<br>
./nctst ./<a href="http://testfile.nc" target="_blank">testfile.nc</a><br>
ncmpi_inq_typeids not implemented<br>
[n-62-12-2:21767] *** Process received signal ***<br>
[n-62-12-2:21767] Signal: Segmentation fault (11)<br>
[n-62-12-2:21767] Signal code: Address not mapped (1)<br>
[n-62-12-2:21767] Failing at address: 0xffffffffffffffe8<br>
[n-62-12-2:21767] [ 0] /lib64/libpthread.so.0(+0xf710)[0x2b3e93945710]<br>
[n-62-12-2:21767] [ 1] /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(std::basic_ostream<char, std::char_traits<char> >::sentry::sentry(std::basic_ostream<char, std::char_traits<char> >&)+0x19)[0x2b3e934ace79]<br>
[n-62-12-2:21767] [ 2] /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)+0x29)[0x2b3e934ad589]<br>
[n-62-12-2:21767] [ 3] /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(std::basic_ostream<char, std::char_traits<char> >& std::operator<< <std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*)+0x27)[0x2b3e934ad9e7]<br>
[n-62-12-2:21767] [ 4] ./nctst[0x40ad62]<br>
[n-62-12-2:21767] [ 5] ./nctst[0x40b93c]<br>
[n-62-12-2:21767] [ 6] /lib64/libc.so.6(__libc_start_main+0xfd)[0x2b3e93d76d5d]<br>
[n-62-12-2:21767] [ 7] ./nctst[0x405899]<br>
[n-62-12-2:21767] *** End of error message ***<br>
<br>
--<br>
Rob Latham<br>
Mathematics and Computer Science Division<br>
Argonne National Lab, IL USA<br>
<br>
<br>
<br>
--<br>
Kind regards Nick<br>
</blockquote>
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</blockquote>
<br>
-- <br>
Rob Latham<br>
Mathematics and Computer Science Division<br>
Argonne National Lab, IL USA<br>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div>Kind regards Nick</div></div></div>
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