Compiling the GACODE in the JET Heimdall computer

[franal12]

Hi GACODE team!

I am planning to compile the gacode on the JET Heimdall computer using the existing makefile JAC-64 in the build directory. I can compile TGLF but am unable to compile any other codes due to an error in the compilation of the math. The compilation error is shown below

mpif90 -module /home/wh4980/gacode/modules -r8  -O1  -fPIC -c math_constants.f90
mpif90 -module /home/wh4980/gacode/modules -r8  -O1  -fPIC -c gauss_legendre.f90
mpif90 -module /home/wh4980/gacode/modules -r8  -O1  -fPIC -c half_hermite.f90
PGF90-S-0038-Symbol, erf, has not been explicitly declared (half_hermite.f90)
  0 inform,   0 warnings,   1 severes, 0 fatal for pseudo_maxwell_pliocene
make: *** [half_hermite.o] Error 2

Any tips on how to resolve this error?
Thanks,
Francis

[jcandy]

@franal12 Is there a version of mpif90 built with gfortran?

[franal12]

@franal12 Is there a version of mpif90 built with gfortran?

Thanks for your response! Yes, a version of openmpi can be loaded along with gfortran.

[jcandy]

Generally for commodity CPU systems I recommend:

• gfortran
• mpich
• openblas (https://www.openblas.net)
• fftw

For openblas use these settings

BINARY=64
USE_THREAD=0
USE_LOCKING=1
NO_SHARED=1
NO_CBLAS=1
NO_LAPACKE=1

Then, the MINT platform setup will be close to what you can use.

[jcandy]

@franal12 Would it be possible to add some minimal credentials to you github profile?

[jcandy]

@franal12 has there been progress?

[franal12]

Hi @jcandy! I compiled the openblas by using the settings mentioned by you and I am getting the following error

test_post_fork.c: In function ‘__ctest_fork_safety_after_fork_in_parent_run’:
test_post_fork.c:79:12: warning: unused variable ‘nthreads_omp’ [-Wunused-variable]
     int i, nthreads_omp;
            ^
cc -O2 -DSMALL_MATRIX_OPT -DUTEST_CHECK -DSANITY_CHECK -DREFNAME=f_ -DMAX_STACK_ALLOC=2048 -DUSE_LOCKING -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DNO_LAPACK -DNO_LAPACKE -DNO_AVX512 -DNO_WARMUP -DMAX_CPU_NUMBER=16 -DMAX_PARALLEL_NUMBER=1 -DBUILD_SINGLE=1 -DBUILD_DOUBLE=1 -DBUILD_COMPLEX=1 -DBUILD_COMPLEX16=1 -DVERSION=\"0.3.26.dev\" -msse3 -mssse3 -msse4.1 -mavx -UASMNAME -UASMFNAME -UNAME -UCNAME -UCHAR_NAME -UCHAR_CNAME -DASMNAME= -DASMFNAME=_ -DNAME=_ -DCNAME= -DCHAR_NAME=\"_\" -DCHAR_CNAME=\"\" -DNO_AFFINITY -I..  -o openblas_utest utest_main.o test_min.o test_amax.o test_ismin.o test_rotmg.o test_axpy.o test_dotu.o test_dsdot.o test_swap.o test_rot.o test_dnrm2.o test_zscal.o test_amin.o test_axpby.o test_fork.o test_post_fork.o ../libopenblas_sandybridge-r0.3.26.dev.a -lm -lm -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/local/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../..  -lgfortran -lm -lquadmath -lm -lc 
test_zscal.o: In function `__ctest_zscal_i_nan_run':
test_zscal.c:(.text+0x40): undefined reference to `cblas_zscal'
test_zscal.o: In function `__ctest_zscal_i_nan_inc_2_run':
test_zscal.c:(.text+0x110): undefined reference to `cblas_zscal'
test_zscal.o: In function `__ctest_zscal_nan_i_run':
test_zscal.c:(.text+0x1e0): undefined reference to `cblas_zscal'
test_zscal.o: In function `__ctest_zscal_nan_i_inc_2_run':
test_zscal.c:(.text+0x2b0): undefined reference to `cblas_zscal'
test_zscal.o: In function `__ctest_zscal_i_inf_run':
test_zscal.c:(.text+0x380): undefined reference to `cblas_zscal'
test_zscal.o:test_zscal.c:(.text+0x450): more undefined references to `cblas_zscal' follow
collect2: error: ld returned 1 exit status
make[1]: *** [openblas_utest] Error 1
make[1]: Leaving directory `/home/wh4980/OpenBLAS-develop/utest'
make: *** [tests] Error 2

I was asking for help from the local IT support so I couldn't get back to you quickly. I updated my profile now on Github.

[jcandy]

I assume libopenblas.a was generated. Can you assume for the moment it's good and try to build GACODE with it?

[franal12]

yes it is generated so I will try to build GACODE and update the thread.

[franal12]

The make file contains the following lines based on the MINT makefile

# Compilers and flags

FC      = mpif90 -fall-intrinsics -std=f2008 -I$(GACODE_ROOT)/modules -J$(GACODE_ROOT)/modules -fPIC
F77     = mpif77
FOMP    =-fopenmp
FMATH   =-fdefault-real-8 -fdefault-double-8
FOPT    =-Ofast
FDEBUG  =-Wall -fcheck=all -fbacktrace -g -ffpe-trap=invalid,zero,overflow -fimplicit-none -finit-real=nan
F2PY    = f2py

# System math libraries
LMATH = /home/wh4980/OpenBLAS-develop/libopenblas.a

# netCDF (not optional any more)
# NETCDF_HOME=/usr/local/depot/netcdf-4.2.1.1/
# NETCDF_DIR is set by the module
NETCDF=-L${NETCDF_DIR}/lib -lnetcdff
NETCDF_INC=${NETCDF_DIR}/include

# Archive 

ARCH = ar cr

and I am getting the following error

mpif90 -module /home/wh4980/gacode/modules -r8  -O1  -fPIC -c math_constants.f90
gfortran: error: unrecognized command line option ‘-module’
gfortran: error: unrecognized command line option ‘-r8’
make: *** [math_constants.o] Error 1

Is there a document or a guide to understand how makefiles are created? I found some guides on the internet but they explain basic makefile syntaxes.

[jcandy]

Is it possible for me to get an account on Heimdall?

[franal12]

I don't think that is possible but we can have a ZOOM meeting and try compiling the Gacode together.

[franal12]

@jcandy
I successfully compiled neo, vgen and tglf but cgyro gives me the following error

Error: Symbol ‘omega_eb’ at (1) has no IMPLICIT type
cgyro_advect_wavenumber.f90:36:40:
 
                  he(j,ir) = omega_eb*h_x(icc+j,in)
                                        1
Error: Rank mismatch in array reference at (1) (2/3)
cgyro_advect_wavenumber.f90:47:23:

Yes, there is a cgyro_globals.mod file in gacode/module. There are many instances of “Rank mismatch” errors.

Compiling gyro gives this error at the end
gfortran: error: gyro_lib.a: No such file or directory
make: [all] Error 1 (ignored)

[jcandy]

Please generate a make log:

$ cd cgyro
$ make clean
$ make &> log.txt

and attach the file here

[franal12]

Here is the log file after cgyro compilation.
log.txt

[jcandy]

Are you using an old version of GACODE (like from 2022?)