Compilation and installation problem

Building Abinit
1

I am having a difficult time installing abinit. My laptop has has an Intel(R) E-2286M Xeon CPU@ 2.40GHz(16CPUs), ~2.4GHz, and 32GB RAM.
I have following the tutorial here (Building Abinit - abinit)carefully, and on this forum as well. When I compile using: …/configure --with-config-file=“alexis.ac”
This is what i get:==============================================================================
=== Final remarks ===

Core build parameters

  • C compiler : gnu version 9.3

  • Fortran compiler : gnu version 9.3

  • architecture : intel xeon (64 bits)

  • debugging : basic

  • optimizations : standard

  • OpenMP enabled : no (collapse: ignored)

  • MPI enabled : yes (flavor: auto)

  • MPI in-place : no

  • MPI-IO enabled : yes

  • GPU enabled : no (flavor: none)

  • LibXML2 enabled : no

  • LibPSML enabled : no

  • XMLF90 enabled : no

  • HDF5 enabled : yes (MPI support: yes)

  • NetCDF enabled : yes (MPI support: no)

  • NetCDF-F enabled : yes (MPI support: no)

  • FFT flavor : fftw3 (libs: user-defined)

  • LINALG flavor : openblas (libs: user-defined)

  • SCALAPACK enabled : no

  • ELPA enabled : no

  • FCFLAGS : -g -ffree-line-length-none -I/usr/include -I/usr/include

  • CPATH :

  • Build workflow : monolith

0 deprecated options have been used:.

Configuration complete.
You may now type “make” to build Abinit.
(or “make -j”, where is the number of available processors)
Then I issue: make -j16, the later make install
When I make this test, I get:
=== Build Information ===
Version : 9.6.2
Build target : x86_64_linux_gnu9.3
Build date : 20211130

=== Compiler Suite ===
C compiler : gnu9.3
C++ compiler : gnu9.3
Fortran compiler : gnu9.3
CFLAGS : -g -O2 -mtune=native -march=native
CXXFLAGS : -g -O2 -mtune=native -march=native
FCFLAGS : -g -ffree-line-length-none -I/usr/include -I/usr/include
FC_LDFLAGS :

=== Optimizations ===
Debug level : basic
Optimization level : standard
Architecture : intel_xeon

=== Multicore ===
Parallel build : /home/alexis/local/
Parallel I/O : yes
openMP support : no
GPU support :

=== Connectors / Fallbacks ===
LINALG flavor : openblas
FFT flavor : fftw3
HDF5 : yes
NetCDF : yes
NetCDF Fortran : yes
LibXC : yes
Wannier90 : no

=== Experimental features ===
Exports :
GW double-precision :

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Default optimizations:
-O2 -mtune=native -march=native

Optimizations for 43_ptgroups:
-O0

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

When I issue : ./runtests.py inside the tests directory, I get:
alexis@Alexis:~/abinit-9.6.2/tests$ ./runtests.py
/home/alexis/abinit-9.6.2/tests/pymods/yaml_tools/init.py:15: UserWarning:
Cannot import numpy or yaml package.
Use pip install numpy pyyaml --user
to install the packages in user mode.
warnings.warn(’\nCannot import numpy or yaml package.\nUse pip install numpy pyyaml --user’
/home/alexis/abinit-9.6.2/tests/pymods/yaml_tools/init.py:24: UserWarning:
Cannot import pandas package. Use pip install pandas --user
to install the package in user mode.
warnings.warn(’\nCannot import pandas package. Use pip install pandas --user’

                    -////-                                                        .`
                   `:////:`                                                   :+ymd-
                  `:::///:`                                             `.:oyhdNdo.
                 .::-:////.                                        `.:osddddddho-

.:+- -:: -////: -:/ysddddhhdddo:.
:shhdNmh- -/: .:///:. . -.o+yhdhddhhhdddyy+:. mo++ydhs:- ::. .////- . ..:-/:////dhhhhhhhhhmhhso/.- hds++++oyyydshhoooos++++++oo+ooo++++s+/ssdmyhhhhyo///yymyhsoy/:..` `::. :+yhhhyyyssooooooosssssssyyyyyyyyyyyo/hyhhsyyhy+oo:-:... `..`` `.` `/:`` -:--/ooooosyyyyyyys+//+oo++/:-://:::/:::` -/. `/::::/:::. -/:`:://::- -/:. .:://:.:/:.` `./:. -/. `//-` `.:/. -/: `/:. `-/:` ` :/: ./: -/. `/- ./- -/: `/:. .:/-` -/:. `./:. -/. `/- `/- -/: `/:. .::-` .:::::::-. -/. `/- `/- -/: -/::- `-/:. ``..`` `.` `.. `.`.:o/-.``.://:-----::::-````. -:-` ``.-.::::/++/+MMMd+oooo++///+ssssooyysysyss++:. ` ` ..-.://+/+/+/::/-.---ydh+ ```.-/+oyyys ``.-:://+/+::-..``` .:/+o/: ``.:://///--.`` . .-////-… .:::-.

Running on Alexis – system Linux – ncpus 16 – Python 2.7.18 – runtests.py-0.6.0
Traceback (most recent call last):
File “./runtests.py”, line 667, in
sys.exit(main())
File “./runtests.py”, line 376, in main
build_env = BuildEnvironment(build_dir_path)
File “/home/alexis/abinit-9.6.2/tests/pymods/testsuite.py”, line 1048, in init
raise e
RuntimeError: Cannot find the ABINIT build tree after 10 trials

and no tutorial on the abinit webpage can run.

Here is my .ac file:
enable_avx_safe_mode=“yes”
with_mpi="/usr"
enable_mpi_io=“yes”
LINALG_LIBS="-L/usr/lib/ -llapack -lblas"
with_libxc=“yes”
LIBXC_CPPFLAGS="-I/usr/include"
LIBXC_FCFLAGS="-I/usr/include"
with_hdf5="/usr"
with_netcdf=“yes”
NETCDF_CPPFLAGS="-I/usr/include/"
NETCDF_FCFLAGS="-I/usr/include/"
NETCDF_LIBS="-L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf -lhdf5_hl -lhdf5 -lpthread -lsz -lz -ldl -lm -lcurl"
with_netcdf_fortran="/usr/include"
NETCDF_FORTRAN_LIBS="-L/usr/lib -lnetcdff -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lnetcdf -lnetcdf"
Any assistance is appreciated in advance.

2

Hi @okelloamollo, you need to run the runtest.py script from the build directory where you compiled abinit. For example, if you build abinit inside abinit/build/ you should run the script inside this directory like so: ../tests/runtests.py [... any options]

I hope this helps!

3

That you fgoudreault, This is the test result;

Suite            failed  passed  succeeded  skipped  disabled  run_etime  tot_etime
atompaw               0       0          0        2         0       0.00       0.00
bigdft                0       0          0       19         0       0.00       0.00
bigdft_paral          0       0          0        4         0       0.00       0.00
built-in              0       0          5        2         0       7.38       7.39
etsf_io               0       0          8        0         0      16.75      16.85
fast                  0       1         10        0         0      32.27      32.52
gpu                   0       0          0        7         0       0.00       0.00
libxc                 1       5         29        0         0     388.97     390.32
mpiio                 0       0          1       16         0       0.83       0.84
paral                 0       8         22      102         0     319.02     319.88
psml                  0       0          0       14         0       0.00       0.00
seq                   0       0          0       18         0       0.00       0.00
tutomultibinit        0       0          3        3         0      22.65      23.98
tutoparal             0       3          1       24         0     150.94     151.04
tutoplugs             0       0          0        4         0       0.00       0.00
tutorespfn            3       6         20        2         0    1603.15    1604.97
tutorial              0       9         50        0         0   -8999.21   -8997.99
unitary               0       1         17       20         0      43.13      43.29
v1                    0       1         73        0         0     167.11     168.23
v2                    0      14         65        0         0     189.63     190.92
v3                    0      12         66        0         0     297.80     300.33
v4                    0      10         51        0         0     276.54     278.29
v5                    0      17         56        0         0     720.74     723.96
v6                    0       7         54        0         0     478.51     480.83
v67mbpt               0      11         14        0         0     247.44     248.62
v7                    0      16         49        0         0     981.81     984.78
v8                    0      16         49        4         0    1285.28    1287.57
v9                    0      13         46        2         0     732.86     734.25
vdwxc                 0       0          0        1         0       0.00       0.00
wannier90             0       0          0        8         0       0.00       0.00

Completed in -983.95 [s]. Average time for test=-1.23 [s], stdev=373.59 [s]
Summary: failed=4, succeeded=689, passed=150, skipped=252, disabled=0

Other tests results are here;

alexis@Alexis:~/abinit-9.6.2/build_gfortran$ make test_fast
cp ./src/98_main/abinit ../tests/built-in/Input/abinit && cd ../tests/built-in/Input && export ABI_PSPDIR="../../Psps_for_tests" && ./abinit testin_fast.abi >& testin_fast.stdout && cat testin_fastt_STATUS && rm -f abinit *DDB *EIG *out* *nc *WFK *abo* *o_* *t_STATUS*

 Status file, reporting on built-in test fast

 ==> The run finished cleanly.
     Moreover, comparison of the total energy, and other (few) relevant quantities with reference values has been successful.
     This does not mean that no problem is present, however. 
     Please run the complete set of ABINIT tests to gain a better confidence in your installation.

Basing on the test, what needs to corrected inorder to do calculations?

4

Well, based on the tests results, it seems your abinit compilation was very successfull! (apart for very few tests that fail) It is common, when building abinit, that some tests fail but mostly you wanna be concerned if a lot of tests fail or if the main feature you want to use abinit for fail. You also wanna check if the parallel build works fine (the paral tests were mostly skipped). You can do this by using the runtests.py -n X argument where X is the number of processes you want to test. I usually set X to 4 because my laptop has 4 cores.