<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Wed, Oct 11, 2017 at 5:29 PM, William T Jones <span dir="ltr"><<a href="mailto:w.t.jones@nasa.gov" target="_blank">w.t.jones@nasa.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I have created an Anaconda Pytyoh 2.7 environment on an SGI-ICE machine and included cython, numpy=1.12, scipy, and mpi4py (based SGI-MPT). While petsc installs fine with:<br>
<br>
% PETSC_CONFIGURE_OPTIONS="--dow<wbr>nload-fblaslapack=1" pip install <a href="https://bitbucket.org/petsc/petsc/get/maint.tar.gz" rel="noreferrer" target="_blank">https://bitbucket.org/petsc/pe<wbr>tsc/get/maint.tar.gz</a><br>
<br>
I cannot get petsc4py to build/install. I am attempting with:<br>
<br>
% export PETSC_DIR=${PREFIX}/envs/myenv<wbr>/lib/python2.7/site-packages/<wbr>petsc<br>
% pip install --no-dependencies petsc4py<br>
<br>
Note, I am using "--no-dependencies" because I want to leave numpy at 1.12 and do not want it to be upgraded. Either way I get the output below. It appears that the link command has been corrupted with the addition of the "gcc" command in the middle of the link command.<br></blockquote><div><br></div><div>/vendor/sgi/mpt/2.14r19/bin/mp<wbr>icc is being called. Does this actually work? I would suspect it of calling 'gcc'<br></div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Any help is appreciated,<br>
<br>
<br>
% pip install --no-dependencies petsc4py<br>
Collecting petsc4py<br>
Using cached petsc4py-3.8.0.tar.gz<br>
Building wheels for collected packages: petsc4py<br>
Running setup.py bdist_wheel for petsc4py ... error<br>
Complete output from command /home/login/anaconda2/envs/mye<wbr>nv/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-bu<wbr>ild-v6lDIk/petsc4py/setup.py';<wbr>f=getattr(tokenize, 'open', open)(__file__);code=f.read().<wbr>replace('\r\n', '\n');f.close();exec(compile(c<wbr>ode, __file__, 'exec'))" bdist_wheel -d /tmp/tmpD2KqLjpip-wheel- --python-tag cp27: <br>
running bdist_wheel <br>
running build <br>
running build_src <br>
running build_py <br>
creating build <br>
creating build/lib.linux-x86_64-2.7 <br>
creating build/lib.linux-x86_64-2.7/pet<wbr>sc4py <br>
copying src/PETSc.py -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py <br>
copying src/__init__.py -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py <br>
copying src/__main__.py -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py <br>
creating build/lib.linux-x86_64-2.7/pet<wbr>sc4py/lib <br>
copying src/lib/__init__.py -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/lib<br>
creating build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include <br>
creating build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/include/petsc4py/petsc4py.<wbr>PETSc.h -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/include/petsc4py/numpy.h -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/include/petsc4py/petsc4py.<wbr>PETSc_api.h -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/include/petsc4py/petsc4py.<wbr>h -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/include/petsc4py/petsc4py.<wbr>i -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/include/petsc4py/__init__.<wbr>pxd -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/include/petsc4py/PETSc.pxd -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/include/petsc4py/__init__.<wbr>pyx -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/PETSc.pxd -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py <br>
copying src/lib/petsc.cfg -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/lib <br>
running build_ext <br>
PETSC_DIR: /home/login/anaconda2/envs/mye<wbr>nv/lib/python2.7/site-packages<wbr>/petsc <br>
PETSC_ARCH: <br>
version: 3.8.0 release <br>
integer-size: 32-bit <br>
scalar-type: real <br>
precision: double <br>
language: CONLY <br>
compiler: /vendor/sgi/mpt/2.14r19/bin/m<wbr>picc <br>
linker: /vendor/sgi/mpt/2.14r19/bin/m<wbr>picc <br>
building 'PETSc' extension <br>
creating build/temp.linux-x86_64-2.7 <br>
creating build/temp.linux-x86_64-2.7/sr<wbr>c <br>
/vendor/sgi/mpt/2.14r19/bin/mp<wbr>icc -pthread -B /home/login/anaconda2/envs/mye<wbr>nv/compiler_compat -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -g -O -fPIC -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -DPETSC_DIR=/home/login/anacon<wbr>da2/envs/myenv/lib/python2.7/<wbr>site-packages/petsc -I/home/login/anaconda2/envs/m<wbr>yenv/lib/python2.7/site-packag<wbr>es/petsc/include -Isrc/include -I/home/login/anaconda2/envs/m<wbr>yenv/lib/python2.7/site-packag<wbr>es/numpy/core/include -I/home/login/anaconda2/envs/m<wbr>yenv/include/python2.7 -c src/PETSc.c -o build/temp.linux-x86_64-2.7/sr<wbr>c/PETSc.o <br>
In file included from /home/login/anaconda2/envs/mye<wbr>nv/lib/python2.7/site-packages<wbr>/numpy/core/include/numpy/<wbr>ndarraytypes.h:1788:0, <br>
from /home/login/anaconda2/envs/mye<wbr>nv/lib/python2.7/site-packages<wbr>/numpy/core/include/numpy/<wbr>ndarrayobject.h:18, <br>
from /home/login/anaconda2/envs/mye<wbr>nv/lib/python2.7/site-packages<wbr>/numpy/core/include/numpy/<wbr>arrayobject.h:4, <br>
from src/include/petsc4py/numpy.h:1<wbr>1, <br>
from src/petsc4py.PETSc.c:519, <br>
from src/PETSc.c:3: <br>
<br>
/home/login/anaconda2/envs/mye<wbr>nv/lib/python2.7/site-packages<wbr>/numpy/core/include/numpy/npy_<wbr>1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] <br>
#warning "Using deprecated NumPy API, disable it by " \ <br>
^ <br>
/vendor/sgi/mpt/2.14r19/bin/mp<wbr>icc -pthread -B /home/login/anaconda2/envs/mye<wbr>nv/compiler_compat -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -g -O -fPIC -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -DPETSC_DIR=/home/login/anacon<wbr>da2/envs/myenv/lib/python2.7/<wbr>site-packages/petsc -I/home/login/anaconda2/envs/m<wbr>yenv/lib/python2.7/site-packag<wbr>es/petsc/include -Isrc/include -I/home/login/anaconda2/envs/m<wbr>yenv/lib/python2.7/site-packag<wbr>es/numpy/core/include -I/home/login/anaconda2/envs/m<wbr>yenv/include/python2.7 -c src/libpetsc4py.c -o build/temp.linux-x86_64-2.7/sr<wbr>c/libpetsc4py.o <br>
/vendor/sgi/mpt/2.14r19/bin/mp<wbr>icc -pthread -B /home/login/anaconda2/envs/mye<wbr>nv/compiler_compat -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -g -O gcc -pthread -shared -B /home/login/anaconda2/envs/mye<wbr>nv/compiler_compat -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -L/home/login/anaconda2/envs/m<wbr>yenv/lib -Wl,-rpath=/home/login/anacond<wbr>a2/envs/myenv/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/sr<wbr>c/PETSc.o build/temp.linux-x86_64-2.7/sr<wbr>c/libpetsc4py.o -L/home/login/anaconda2/envs/m<wbr>yenv/lib/python2.7/site-packag<wbr>es/petsc/lib -L/home/login/anaconda2/envs/m<wbr>yenv/lib -Wl,-rpath,/home/login/anacond<wbr>a2/envs/myenv/lib/python2.7/<wbr>site-packages/petsc/lib -Wl,-rpath,/home/login/anacond<wbr>a2/envs/myenv/lib -lpetsc -lpython2.7 -o build/lib.linux-x86_64-2.7/pet<wbr>sc4py/lib/PETSc.so <br>
gcc: error: gcc: No such file or directory <br>
error: command '/vendor/sgi/mpt/2.14r19/bin/m<wbr>picc' failed with exit status 1<br>
<br>
<br>
------------------------------<wbr>---------- <br>
Failed building wheel for petsc4py <br>
Running setup.py clean for petsc4py <br>
Failed to build petsc4py <br>
Installing collected packages: petsc4py <br>
Running setup.py install for petsc4py ... error <br>
Complete output from command /home/login/anaconda2/envs/mye<wbr>nv/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-bu<wbr>ild-v6lDIk/petsc4py/setup.py';<wbr>f=getattr(tokenize, 'open', open)(__file__);code=f.read().<wbr>replace('\r\n', '\n');f.close();exec(compile(c<wbr>ode, __file__, 'exec'))" install --record /tmp/pip-d6NYW8-record/install<wbr>-record.txt --single-version-externally-ma<wbr>naged --compile: <br>
running install <br>
running build <br>
running build_src <br>
running build_py <br>
creating build <br>
creating build/lib.linux-x86_64-2.7 <br>
creating build/lib.linux-x86_64-2.7/pet<wbr>sc4py <br>
copying src/PETSc.py -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py <br>
copying src/__init__.py -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py <br>
copying src/__main__.py -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py <br>
creating build/lib.linux-x86_64-2.7/pet<wbr>sc4py/lib <br>
copying src/lib/__init__.py -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/lib<br>
creating build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include <br>
creating build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/include/petsc4py/petsc4py.<wbr>PETSc.h -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/include/petsc4py/numpy.h -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/include/petsc4py/petsc4py.<wbr>PETSc_api.h -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/include/petsc4py/petsc4py.<wbr>h -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/include/petsc4py/petsc4py.<wbr>i -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/include/petsc4py/__init__.<wbr>pxd -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/include/petsc4py/PETSc.pxd -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/include/petsc4py/__init__.<wbr>pyx -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/include/petsc4py <br>
copying src/PETSc.pxd -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py <br>
copying src/lib/petsc.cfg -> build/lib.linux-x86_64-2.7/pet<wbr>sc4py/lib<br>
running build_ext <br>
PETSC_DIR: /home/login/anaconda2/envs/mye<wbr>nv/lib/python2.7/site-packages<wbr>/petsc <br>
PETSC_ARCH: <br>
version: 3.8.0 release <br>
integer-size: 32-bit <br>
scalar-type: real <br>
precision: double <br>
language: CONLY <br>
compiler: /vendor/sgi/mpt/2.14r19/bin/m<wbr>picc <br>
linker: /vendor/sgi/mpt/2.14r19/bin/m<wbr>picc <br>
building 'PETSc' extension <br>
creating build/temp.linux-x86_64-2.7 <br>
creating build/temp.linux-x86_64-2.7/sr<wbr>c <br>
/vendor/sgi/mpt/2.14r19/bin/mp<wbr>icc -pthread -B /home/login/anaconda2/envs/mye<wbr>nv/compiler_compat -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -g -O -fPIC -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -DPETSC_DIR=/home/login/anacon<wbr>da2/envs/myenv/lib/python2.7/<wbr>site-packages/petsc -I/home/login/anaconda2/envs/m<wbr>yenv/lib/python2.7/site-packag<wbr>es/petsc/include -Isrc/include -I/home/login/anaconda2/envs/m<wbr>yenv/lib/python2.7/site-packag<wbr>es/numpy/core/include -I/home/login/anaconda2/envs/m<wbr>yenv/include/python2.7 -c src/PETSc.c -o build/temp.linux-x86_64-2.7/sr<wbr>c/PETSc.o <br>
In file included from /home/login/anaconda2/envs/mye<wbr>nv/lib/python2.7/site-packages<wbr>/numpy/core/include/numpy/<wbr>ndarraytypes.h:1788:0, <br>
from /home/login/anaconda2/envs/mye<wbr>nv/lib/python2.7/site-packages<wbr>/numpy/core/include/numpy/<wbr>ndarrayobject.h:18, <br>
from /home/login/anaconda2/envs/mye<wbr>nv/lib/python2.7/site-packages<wbr>/numpy/core/include/numpy/<wbr>arrayobject.h:4, <br>
from src/include/petsc4py/numpy.h:1<wbr>1, <br>
from src/petsc4py.PETSc.c:519,<br>
from src/PETSc.c:3:<br>
<br>
/home/login/anaconda2/envs/mye<wbr>nv/lib/python2.7/site-packages<wbr>/numpy/core/include/numpy/npy_<wbr>1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]<br>
#warning "Using deprecated NumPy API, disable it by " \<br>
^<br>
/vendor/sgi/mpt/2.14r19/bin/mp<wbr>icc -pthread -B /home/login/anaconda2/envs/mye<wbr>nv/compiler_compat -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -g -O -fPIC -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -DPETSC_DIR=/home/login/anacon<wbr>da2/envs/myenv/lib/python2.7/<wbr>site-packages/petsc -I/home/login/anaconda2/envs/m<wbr>yenv/lib/python2.7/site-packag<wbr>es/petsc/include -Isrc/include -I/home/login/anaconda2/envs/m<wbr>yenv/lib/python2.7/site-packag<wbr>es/numpy/core/include -I/home/login/anaconda2/envs/m<wbr>yenv/include/python2.7 -c src/libpetsc4py.c -o build/temp.linux-x86_64-2.7/sr<wbr>c/libpetsc4py.o<br>
/vendor/sgi/mpt/2.14r19/bin/mp<wbr>icc -pthread -B /home/login/anaconda2/envs/mye<wbr>nv/compiler_compat -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -g -O gcc -pthread -shared -B /home/login/anaconda2/envs/mye<wbr>nv/compiler_compat -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -L/home/login/anaconda2/envs/m<wbr>yenv/lib -Wl,-rpath=/home/login/anacond<wbr>a2/envs/myenv/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/sr<wbr>c/PETSc.o build/temp.linux-x86_64-2.7/sr<wbr>c/libpetsc4py.o -L/home/login/anaconda2/envs/m<wbr>yenv/lib/python2.7/site-packag<wbr>es/petsc/lib -L/home/login/anaconda2/envs/m<wbr>yenv/lib -Wl,-rpath,/home/login/anacond<wbr>a2/envs/myenv/lib/python2.7/<wbr>site-packages/petsc/lib -Wl,-rpath,/home/login/anacond<wbr>a2/envs/myenv/lib -lpetsc -lpython2.7 -o build/lib.linux-x86_64-2.7/pet<wbr>sc4py/lib/PETSc.so<br>
gcc: error: gcc: No such file or directory<br>
error: command '/vendor/sgi/mpt/2.14r19/bin/m<wbr>picc' failed with exit status 1<br>
<br>
------------------------------<wbr>----------<br>
Command "/home/login/anaconda2/envs/my<wbr>env/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-bu<wbr>ild-v6lDIk/petsc4py/setup.py';<wbr>f=getattr(tokenize, 'open', open)(__file__);code=f.read().<wbr>replace('\r\n', '\n');f.close();exec(compile(c<wbr>ode, __file__, 'exec'))" install --record /tmp/pip-d6NYW8-record/install<wbr>-record.txt --single-version-externally-ma<wbr>naged --compile" failed with error code 1 in /tmp/pip-build-v6lDIk/petsc4py<wbr>/<span class="gmail-HOEnZb"><font color="#888888"><br>
<br>
<br>
-- <br>
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-<wbr>=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-<wbr>=-=-=-=-=-=-<br>
<br>
Bill Jones <a href="mailto:W.T.JONES@NASA.GOV" target="_blank">W.T.JONES@NASA.GOV</a><br>
Mail Stop 128 Computational AeroSciences Branch<br>
15 Langley Boulevard Research Directorate<br>
NASA Langley Research Center Building 1268, Room 1044<br>
Hampton, VA 23681-2199 Phone <a href="tel:%2B1%20757%20864-5318" value="+17578645318" target="_blank">+1 757 864-5318</a><br>
Fax <a href="tel:%2B1%20757%20864-8816" value="+17578648816" target="_blank">+1 757 864-8816</a><br>
<a href="http://fun3d.larc.nasa.gov" rel="noreferrer" target="_blank">http://fun3d.larc.nasa.gov</a><br>
</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.caam.rice.edu/~mk51/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div>
</div></div>