[MMTK] MMTK installation problem

DmitryASuplatov genesup at gmail.com
Tue Mar 24 10:03:28 UTC 2015


RESOLVED

If you have the same problem you can try this before compiling:
export CPPFLAGS=-I/usr/lib64/python2.7/site-packages/numpy/core/include

Also for the newbies in MMTK like me I would like to repeat the 
installation sequence which has worked for me:

1. install numpy (in opensuse use yast; I installed both python-numpy 
and python-numpy-devel packs)
2. install netcdf (in opensuse use yast; I installed both netcdf and 
netcdf-devel packs)
3. install ScientificPython from sources (beware that at first I did the 
step 3 without step 2 and got an error only at step 5)
4. export CPPFLAGS=-I/usr/lib64/python2.7/site-packages/numpy/core/include
5. install MMTK from sources

Best,
Dmitry

On 03/24/2015 12:21 PM, DmitryASuplatov wrote:
> Hello,
>
> I am trying to install MMTK on opensuse 13.1 x86_64 (python2.7).
>
> The command "python setup.py build" returns the following error:
> ----------------------------------------------------------------------------------------
> gcc -pthread -fno-strict-aliasing -fmessage-length=0 
> -grecord-gcc-switches -fstack-protector -O2 -Wall -D_FORTIFY_SOURCE=2 
> -funwind-tables -fasynchronous-unwind-tables -g -DNDEBUG 
> -fmessage-length=0 -grecord-gcc-switches -fstack-protector -O2 -Wall 
> -D_FORTIFY_SOURCE=2 -funwind-tables -fasynchronous-unwind-tables -g 
> -DOPENSSL_LOAD_CONF 
> -I*/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/* -fPIC 
> -DLIBM_HAS_ERFC -D_LONG64_ -DEXTENDED_TYPES -IInclude 
> -I/usr/lib/python2.7/site-packages/numpy/core/include 
> -I/usr/include/python2.7 -c Src/MMTK_DCD.c -o 
> build/temp.linux-x86_64-2.7/Src/MMTK_DCD.o 
> -DUSE_NETCDF_H_FROM_SCIENTIFIC=1 -DNUMPY=1
> In file included from Include/MMTK/core.h:11:0,
>                  from Include/MMTK/universe.h:9,
>                  from Src/MMTK_DCD.c:8:
> Include/MMTK/arrayobject.h:2:30: fatal error: numpy/oldnumeric.h: No 
> such file or directory
>  #include "numpy/oldnumeric.h"
> ----------------------------------------------------------------------------------------
>
> However, the file in question indeed exists in the include folder 
> provided to the compiler (see the bold text above):
> ----------------------------------------------------------------------------------------
> -rw-r--r-- 1 root root 680 Apr  7  2013 
> /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/oldnumeric.h
> ----------------------------------------------------------------------------------------
>
> Could you suggest what is my mistake?
> And just to avoid confusion - I have no specific interest in numpy, so 
> if any other package could be used instead to make MMTK work it would 
> be totally OK with me.
>
> Thank you very much for your time,
>
> Best,
> Dmitry
>
> --
> Dr. Dmitry Suplatov
> Senior research scientist
> Bioinformatics and structural biology group
> Department of Biokinetics
> Belozersky Institute of Physicochemical Biology
> Lomonosov Moscow State University
> 1-73 Lenin Hills, 119991 Moscow, Russia
> Cell:  +7.903.975.34.22
> Phone/Fax:  +7.495.939.46.53
> E-mail:d.a.suplatov at gmail.com
> E-mail:d.a.suplatov at belozersky.msu.ru
>

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