<div dir="ltr">Hi,<div><br></div><div>That issue likely relates to the (wrapper) compiler not handling some aspect of OpenMP correctly (from the "pomp" string). Likely the solution is outside GROMACS space.</div>
<div><br></div><div>Mark</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Aug 1, 2014 at 7:56 AM, Theodore Si <span dir="ltr"><<a href="mailto:sjyzhxw@gmail.com" target="_blank">sjyzhxw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I edited that file, and some other files, all the same problem(I wonder why just 3 or 4 files have that problem). I can compile now.<br>
Howerver, a new problem has arisen:<br>
<br>
../../lib/libgromacs_mpi.so.0.<u></u>0.0: undefined reference to `pomp_rd_table'<br>
../../lib/libgromacs_mpi.so.0.<u></u>0.0: undefined reference to `POMP_MAX_ID'<br>
collect2: ld returned 1 exit status<br>
make[2]: *** [bin/template] Error 1<br>
make[1]: *** [share/template/CMakeFiles/<u></u>template.dir/all] Error 2<div class=""><br>
make: *** [all] Error 2<br>
<br>
<br></div>
于2014年8月1日 18:16:36,Theodore Si写到:<div class="HOEnZb"><div class="h5"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I tried to merge them to one line, it worked.<br>
But there are many multi-line comments, it is impossible to change<br>
them one by one.<br>
<br>
<br>
于2014年8月1日 17:38:28,Erik Lindahl写到:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Try adding a backslash at the end of line 24.<br>
<br>
Cheers,<br>
<br>
Erik<br>
<br>
On 01 Aug 2014, at 11:09, Theodore Si <<a href="mailto:sjyzhxw@gmail.com" target="_blank">sjyzhxw@gmail.com</a><br>
<mailto:<a href="mailto:sjyzhxw@gmail.com" target="_blank">sjyzhxw@gmail.com</a>>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
<br>
Does anyone know the instrumentation tool Vampir Trace? I am using<br>
it, and I want to instrument the gromacs code.<br>
So my cmake options are:<br>
<br>
cmake .. -DCMAKE_BUILD_OWN_FFTW=ON -DCMAKE_C_COMPILER=vtcc<br>
-DCMAKE_CXX_COMPILER=vtcxx -DGMX_MPI=on<br>
-DCMAKE_INSTALL_PREFIX=/home/<u></u>theo/gmx<br>
-CUDA_TOOLKIT_ROOT_DIR=/usr/<u></u>local/cuda-5.5<br>
<br>
Vampir Trace includes some binaries, like vtcc and vtcxx above. They<br>
behave like compiler but are actually compiler wrapper.<br>
For example, you can write main.c and vtcc main.c -o main, and the<br>
binary main will be built and you can run it like a normal binary<br>
file, but during the run, some files will be generated and can be<br>
analysed latter.<br>
<br>
However, error occurs:<br>
<br>
[ 2%] Building C object<br>
src/gromacs/CMakeFiles/<u></u>libgromacs.dir/__/external/<u></u>tng_io/src/compression/tng_<u></u>compress.c.o<br>
<br>
/home/theo/gromacs-5.0/src/<u></u>external/tng_io/src/<u></u>compression/tng_compress.c:25:<br>
<br>
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘speed’<br>
/home/theo/gromacs-5.0/src/<u></u>external/tng_io/src/<u></u>compression/tng_compress.c:<br>
<br>
In function ‘quantize’:<br>
/home/theo/gromacs-5.0/src/<u></u>external/tng_io/src/<u></u>compression/tng_compress.c:80:<br>
<br>
warning: implicit declaration of function ‘verify_input_data’<br>
At top level:<br>
cc1: warning: unrecognized command line option<br>
"-Wno-maybe-uninitialized"<br>
make[2]: ***<br>
[src/gromacs/CMakeFiles/<u></u>libgromacs.dir/__/external/<u></u>tng_io/src/compression/tng_<u></u>compress.c.o]<br>
<br>
Error 1<br>
make[1]: *** [src/gromacs/CMakeFiles/<u></u>libgromacs.dir/all] Error 2<br>
make: *** [all] Error 2<br>
<br>
When I open the tng_compress.c, I find that line 25 is just a comment.<br>
<br>
24 #define SPEED_DEFAULT 2 /* Default to relatively fast compression.<br>
For very good compression it makes sense to<br>
25 choose speed=4 or speed=5 */<br>
26<br>
<br>
Could you tell me what's going on?<br>
<br>
I'd appreciate you kind help.<br>
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