Dalton2015-make compilation error

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Dalton2015-make compilation error

Post by bcramer » 13 Aug 2016, 15:01

Dear colleagues,
Installing Dalton I received some compilation errors listed in the attachment and resumed bellow.
(The PC is operated with OPenSUSE 12.3 32b, OpenMPI 1.4.5 and Intel Composer-xe-2011)
make --> errors
/usr/include/c++/4.7/ext/atomicity.h(48): error: identifier "__ATOMIC_ACQ_REL" is undefined
{ return __atomic_fetch_add(__mem, __val, __ATOMIC_ACQ_REL); }
etc................ ^

make[2]: *** [CMakeFiles/geooptlib.dir/LSDALTON/geomopt/dqdx.cpp.o] Error 2
make[1]: *** [CMakeFiles/geooptlib.dir/all] Error 2
make: *** [all] Error 2
The dalton executables `dalton dalton.x` where generated but running the test files with make test all failed.
The missing library libcilkrts.so.5 is not part of gcc-4.7 lib and I could not find any gcc version for 32bit.

Any help is wellcome.
Thank you
DALTON 2015 installation sequence.pdf
(17.66 KiB) Downloaded 451 times

Posts: 600
Joined: 15 Oct 2013, 05:37
First name(s): Peter
Middle name(s): Robert
Last name(s): Taylor
Affiliation: Tianjin University
Country: China

Re: Dalton2015-make compilation error

Post by taylor » 13 Aug 2016, 15:49

You would appear to have some problem with your software stack independent of Dalton/LSDalton. The error you flagged in your message is quite clearly a problem with the compiler/libraries installation on your software system and for the life of me I do not see how gcc-4.7 (nor any version!) is relevant: you are compiling with the Intel compiler suite! The CILK library should be part of this. I strongly suspect your build environment has got itself confused. Your PDF attachment is useless: I will not download a file when a user could simply post an output that could be read immediately, rather than my having to download it and then using Acrobat (which is what my browser(s) insist on doing), just by the user posting the output of their build.

The GNU compiler stuff should not be any part of this. Possibly your system's environment is messed up, or possibly yours, but while the calling sequences between GNU and Intel are now standardized, one cannot expect them to use the same names for the same things. It would be nice, but it's not going to happen. I believe that at the compilation and linking stage, at least until you get to the maths libraries, you must go with one or the other.

I repeat: I do not believe this is a Dalton/LSDalton problem. The compiler (2011) is getting a bit long in the tooth, but for historical reasons I still have access to it and I get no problems building under Centos 6, for example. On the other hand, OpenMPI 1.4.x is prehistoric, and I don't really understand why you are trying to build Dalton2015 when Dalton2016 is available. We do not have the personpower (remember, this is a purely volunteer organization) to support old versions of the code, together with compiling with old versions of the compilers, together with old versions of the libraries like OpenMPI. I am rather afraid the solution to your problem lies within your setup, and I do not see how, unless someone other than me has an "aha! I remember this from years ago!" moment, we can do much to sort this out.

Best regards

Posts: 600
Joined: 15 Oct 2013, 05:37
First name(s): Peter
Middle name(s): Robert
Last name(s): Taylor
Affiliation: Tianjin University
Country: China

Re: Dalton2015-make compilation error

Post by taylor » 13 Aug 2016, 16:00

P.S. As I mentioned we use Centos 6 as our main operating system at home, but we have a separate box where we test newer operating systems in VMs under Centos 7. And our OpenSUSE test/evaluation system is Leap 42.1 which sounds quite a bit newer than your Open SuSE 12. I know very little about OpenSuSE, we just try to stay on the breaking wave as Linux systems (Debian, Ubuntu, other nasty variants...) evolve, but I wonder how up-to-date your system is? I recognize this may not be under your control --- many people are stuck with whatever "central computing" or "central IT" provide/support. But I have to say I don't have a lot of confidence in your software stack...

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Re: Dalton2015-make compilation error

Post by bast » 14 Aug 2016, 20:22

dear Bruno,

I recommend to first try to compile a C++ hello world program, e.g.:
http://groups.engin.umd.umich.edu/CIS/c ... world.html

Save it to a file (hello.cpp) and try to compile it with:

Code: Select all

$ icpc hello.cpp
does that work? I suspect that this will fail and then you can debug
this problem independently of Dalton.

best wishes,

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