Comments (8)
mbkumar
commented on June 26, 2024
Could you please follow the steps posted at https://github.com/PrincetonUniversity/SPEC/wiki/Stellar-Compilation-Instructions and see if those instructions help?
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jonathanschilling
commented on June 26, 2024
I got the Makefile setup for building the python wrapper to work again.
Here are the steps to reproduce this.
- Clone the latest state of Caoxiang's
f90wrapand install it:git clone [email protected]:zhucaoxiang/f90wrap.git cd f90wrap pip install --user .
- I assume that you start from a clean clone of the SPEC repository on the
pywrap_makefilebranch:
git clone [email protected]:PrincetonUniversity/SPEC.git -b pywrap_makefile SPEC_pywrap_makefile - Go into the
python_wrapperdirectory:
cd SPEC_pywrap_makefile/Utilities/python_wrapper - Build SPEC itself and the Python wrapper (make sure to adjust BUILD_ENV to your targeted machine):
make BUILD_ENV=gfortran_arch
At the end, the SPEC version should be printed:... lots of messages ... SPEC version: 3.1 - Check the setup:
- Check that the version output works on the command line:
python -c "from spec import spec; print('SPEC version: {:}'.format(spec.constants.version))" - Check that SPEC can be run in stand-alone mode via the Python wrapper:
python spec/core.py ../../InputFiles/TestCases/G3V01L0Fi.001.sp - Check that the first example (optimization) for the Python wrapper works:
python examples/example.py - Check that the second example (iterative re-convergence) for the Python wrapper works:
OMP_NUM_THREADS=1 python examples/example_2.py
- Check that the version output works on the command line:
@abaillod @zhucaoxiang
Can you please check if this works on your machines as well?
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abaillod
commented on June 26, 2024
@mbkumar, I am not sure to fully understand your link, especially point 6. As I said, I am a beginner with cmake and I have no idea what I am doing when I modify these files. Anyway since the Makefile seems to be fixed I will work with that. I am happy to test the cmake on my machine though if needed!
@jonathanschilling , thanks for fixing the Makefile! I however had to do some changes so that it works on my machine. I did the following changes:
@@ -7,11 +7,11 @@ include ${SOURCES}/SPECfile
# define the compiler names
#=======================================================================
-CC = gcc
+#CC = gcc
# Fortran compiler
-F90 = gfortran
-#F90 = ifort
+#F90 = gfortran
+F90 = ifort
#F90 = /opt/intel/composer_xe_2015.3.187/bin/intel64/ifort
PYTHON = python3
@@ -28,16 +28,14 @@ ifeq ($(F90),gfortran)
endif
ifeq ($(F90),ifort)
- # gfortran f90wrap temp files only. not compilation
- FPP = gfortran -E
-
- FPP_F90FLAGS = -x f95-cpp-input -fPIC
-
- # use 1 and 0 for True and False
- F90FLAGS = -fpscomp logicals -fPIC
-
- # for f2py
- FCOMP = intelem
+ FPP = gfortran -E # gfortran f90wrap temp files only. not compilation
+ FPP_F90FLAGS = -x f95-cpp-input -fPIC
+ F90FLAGS = -fpscomp logicals -fPIC # use 1 and 0 for True and False
+ FCOMP = intelem # for f2py
+ LINKS=-L${MKLROOT}/lib/intel64 -lmkl_rt -lpthread -lm -ldl
+ LINKS+=-L$(HDF5_HOME)/lib -lhdf5_fortran -lhdf5 -lpthread -lz -lm
+ LINKS+=-L$(FFTW_DIR)/lib -lfftw3
+ LINKS+=-liomp5
endif
#=======================================================================
Then all the tests you propose were successful!
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jonathanschilling
commented on June 26, 2024
@abaillod Great to hear that this setup works for you! Can you maybe modify the Makefile in python_wrapper in a similar way as done in the SPECfile where flags are selected based on BUILD_ENV so that we do not need to edit it all the time?
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zhucaoxiang
commented on June 26, 2024
@jonathanschilling @abaillod I pushed one commit to adopt the Intel compiler. Now, you can use something like make all BUILD_ENV=intel_stellar F90=ifort.
But I do have a question testing python spec/core.py ../../InputFiles/TestCases/G3V01L0Fi.001.sp, while I can run xspec normally. I got the following error.
Invalid line in screenlist: Wpp00aa = T
readin : :
readin : ********** : Igeometry= 3 ; Istellsym= 1 ; Lreflect= 0 ;
readin : : Lfreebound= 0 ; phiedge= 2.000000000000000E+00 ; curtor= 1.038123580200000E-09 ; curpol= 0.000000000000000E+00 ;
readin : : gamma= 0.000000000000000E+00 ;
readin : : Nfp= 5 ; Nvol= 1 ; Mvol= 1 ; Mpol= 4 ; Ntor= 4 ;
readin : : pscale= 0.00000E+00 ; Ladiabatic= 0 ; Lconstraint= 0 ; mupf: tol,its= 1.00E-12 , 128 ;
readin : : Lrad = 8,
readin : :
readin : ********** : Linitialize= 0 ;LautoinitBn= 1 ; Lzerovac= 0 ; Ndiscrete= 2 ;
readin : : Nquad= -1 ; iMpol= -4 ; iNtor= -4 ;
readin : : Lsparse= 0 ; Lsvdiota= 0 ; imethod= 3 ; iorder= 2 ; iprecon= 1 ; iotatol= -1.00000E+00 ;
readin : : Lextrap= 0 ; Mregular= -1 ; Lrzaxis= 1 ; Ntoraxis= 3 ;
readin : :
readin : ********** : LBeltrami= 4 ; Linitgues= 1 ; Lmatsolver= 3 ; LGMRESprec= 1 ; NiterGMRES= 200 ; epsGMRES= 1.00000E-14 ; epsILU= 1.00000E-12 ;
readin : :
readin : ********** : Lfindzero= 2 ;
readin : : escale= 0.00000E+00 ; opsilon= 1.00000E+00 ; pcondense= 4.000 ; epsilon= 1.00000E+00 ; wpoloidal= 1.0000 ; upsilon= 1.00000E+00 ;
readin : : forcetol= 1.00000E-12 ; c05xmax= 1.00000E-06 ; c05xtol= 1.00000E-12 ; c05factor= 1.00000E-04 ; LreadGF= F ;
readin : : mfreeits= 0 ; gBntol= 1.00000E-06 ; gBnbld= 6.66000E-01 ;
readin : : vcasingeps= 1.00000E-12 ; vcasingtol= 1.00000E-08 ; vcasingits= 8 ; vcasingper= 1 ;
readin : :
readin : ********** : odetol= 1.00E-07 ; nPpts= 500 ;
readin : : LHevalues= F ; LHevectors= F ; LHmatrix= F ; Lperturbed= 0 ; dpp= -1 ; dqq= -1 ; dRZ= 1.00000000E-05 ; Lcheck= 0 ; Ltiming= F ;
readin : :
readin : : myid= 0 ; Rscale= 1.000000000000000E+01 ;
preset : : myid= 0 ; Mrad= 8 : Lrad= 8,
preset : ********** : LBsequad= F , LBnewton= F , LBlinear= T ;
preset : :
preset : ********** : Nquad= -1 ; mn= 41 ; NGdof= 0 ; NAdof= 361,
preset : :
preset : ********** : Nt= 32 ; Nz= 32 ; Ntz= 1024 ;
INTEL MKL ERROR: /opt/intel/oneapi/mkl/2021.1.1/lib/intel64/libmkl_avx512.so.1: undefined symbol: mkl_sparse_optimize_bsr_trsm_i8.
Intel MKL FATAL ERROR: Cannot load libmkl_avx512.so.1 or libmkl_def.so.1.
srun: error: stellar-k08n20: task 0: Exited with exit code 2
srun: launch/slurm: _step_signal: Terminating StepId=96299.0
The first line is interesting. It doesn't show in the xspec execution. The error seems happening with a linking error, so there must be an error. Do you guys have any clue? (I think I might have some issues with my mpi4py)
- I think Jonathan's fix breaks CMAKE that @mbkumar set up. My understanding is that the CMAKE system or the
steup.pyscript is compiling a library/package namedspecand put it in the/specfolder. That's why it was usingimport spec.spec as specincore.py. Right now, the import line is different. I haven't tested it on my side, but I guess thepython setup.py installway doesn't work.
I didn't push a fix because a) I was waiting for the merge of my f90warp fork; b) a solution works for both Makefile and CMAKE. But I think we are really close. (Just use a consistent name on both sides).
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jonathanschilling
commented on June 26, 2024
@zhucaoxiang I think we should keep the adjusted name of the auto-generated Python wrapper as "spec_f90wrapped".
Otherwise, I feel that we have too many slightly different items named "spec" in this setup.
@mbkumar Can you adjust the CMake setup to use this different name?
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mbkumar
commented on June 26, 2024
I have no issues with using different names if that reduces confusion for
everyone.
I'll push a fix.
Bharat Medasani
Engineer
Princeton Plasma Physics Lab (PPPL)
…On Mon, Jan 24, 2022 at 6:14 AM Jonathan Schilling ***@***.***> wrote:
@zhucaoxiang <https://github.com/zhucaoxiang> I think we should keep the
adjusted name of the auto-generated Python wrapper as "spec_f90wrapped".
Otherwise, I feel that we have too many slightly different items named
"spec" in this setup.
@mbkumar <https://github.com/mbkumar> Can you adjust the CMake setup to
use this different name?
—
Reply to this email directly, view it on GitHub
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abaillod
commented on June 26, 2024
This issue has been solved on my machine thanks to the recent fixes proposed by @jonathanschilling. I am closing it!
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Related Issues (20)
- GMRES error HOT 10
- Segmentation faults when compiled with cmake HOT 6
- Problem with master branch HOT 4
- Issue when restarting from .end file HOT 6
- Help needed to install python wrappers HOT 15
- Wrapper will not compile (reserved python words?) HOT 3
- Problem running tests on master branch HOT 3
- python_wrapper Makefile setup HOT 2
- Question about force-gradient HOT 4
- Bug in force gradient when Lrzaxis=1 ?
- MATLAB metric subroutine needs fix HOT 2
- Python wrapper compilation for Henneberg representation branch HOT 2
- VMEC initializer HOT 2
- Read initial guess with python wrappers HOT 5
- Cannot install f90wrap HOT 7
- Question about matrix free method HOT 2
- SPEC license? HOT 5
- Installation on mac m1 HOT 16
- py_spec installation is borken HOT 1
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