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--- admin:compilaciones:abinit [2026/02/10 16:48] – created bbruzzo
+++ admin:compilaciones:abinit [2026/02/13 18:00] (current) – ldd check bbruzzo
@@ Line 16: / Line 16: @@
 </code>
-===== Compilación =====
+===== Parche =====
 El usuario que solicita el software nos indica que hay un bug que es necesario parchear.
@@ Line 23: / Line 23: @@
 Verifiquemos que la línea que el usuario quiere modificar se encuentra intacta en la nueva release, es decir,
 que el bug no fue corregido en la versión release.
+El usuario reporta:o
+//
+Hay un bug que se debe modificar manualmente: Dentro de la carpeta principal del código (abinit-X.X.X, 10.4.7 es la última versión) uno se encuentra con el directorio scr/, dentro del directorio scr/ uno debe dirigirse al directorio 56_recipspace/, el archivo a editar se llama m_gsphere.F90.
+La línea 593 de este archivo reza vec(3) = n1_max(dir3), pero debería ser: vec(3) = n3_max(dir3)//
+<code>cd src/56_recipspace/</code>
+La nueva release es la versión 10.6.3. En ella la línea indicada por el usuario ahora es la línea 585:
+<code>[bbruzzo@snmgt01 56_recipspace]$ grep -n "vec(3) ="  -B 2 -A 12  m_gsphere.F90
+- ecut = HUGE(one)
+- do dir3=1,3
+:   vec(3) = n1_max(dir3)
+-   do dir2=1,3
+-     vec(2) = n2_max(dir2)
+-     do dir1=1,3
+-       vec(1) = n1_max(dir1)
+-       if (ANY(vec/=0)) then
+-         trial_ene = half * normv(vec,Cryst%gmet,"G")**2
+-         ecut = MIN(ecut,trial_ene)
+-         !write(std_out,*)vec(:),trial_ene
+-       end if
+-     end do
+-   end do
+- end do
+</code>
+Aplicamos parche:
+<code>sed -i 's/vec(3) = n1_max(dir3)/vec(3) = n3_max(dir3)/' m_gsphere.F90</code>
+Volvemos al root path del software.
+<code>cd ../.. </code>
+===== Compilación =====
+El usuario nos brindó esta configuración:
+<code>../configure
+--prefix="/home/juan/MAMBA/abinit-9.10.5/build_intel+wann3.1.0"
+FC=mpiifort
+CC=mpiicc
+CXX=mpiicpc
+--with-libxc="/home/juan/MAMBA/abinit-9.10.5/build_intel+wannier90/fallbacks/install_fb/intel/2021.6/libxc/6.0.0"
+--with-hdf5="/home/juan/MAMBA/abinit-9.10.5/build_intel+wannier90/fallbacks/install_fb/intel/2021.6/hdf5/1.10.8"
+--with-netcdf="/home/juan/MAMBA/abinit-9.10.5/build_intel+wannier90/fallbacks/install_fb/intel/2021.6/netcdf4/4.9.0"
+--with-netcdf-fortran="/home/juan/MAMBA/abinit-9.10.5/build_intel+wannier90/fallbacks/install_fb/intel/2021.6/netcdf4_fortran/4.6.0"
+--with-xmlf90="/home/juan/MAMBA/abinit-9.10.5/build_intel+wannier90/fallbacks/install_fb/intel/2021.6/xmlf90/1.5.6"
+--with-libpsml="/home/juan/MAMBA/abinit-9.10.5/build_intel+wannier90/fallbacks/install_fb/intel/2021.6/libpsml/1.1.12"
+--with-wannier90=/home/juan/wannier90-3.1.0
+--with-libxml2="/home/juan/local"
+XML2_CONFIG="/home/juan/local/bin/xml2-config"
+--enable-mpi-inplace</code>
+Pero también vamos a usar la documentación oficial para construir nuestra propia:
+https://docs.abinit.org/installation/
+==== Preparación de enviroment ====
+<code>
+module purge
+module load intel openmpi5
+</code>
+ABINIT tiene una interfaz de Python, elijo usar un enviroment:
+Python:
+<code>
+micromamba create -n myenv python=3.10
+micromamba activate myenv
+</code>
+==== Config ====
+Copiamos el archivo de configuración template con el nombre snmgt01.ac9.
+<code>cp doc/build/config-template.ac9 snmgt01.ac9</code>
+=== HDF5 ===
+La versión de HDF5 tanto del modulo hdf5 como de phdf5 me está fallando al hacer configure, voy a probar [[hdf5|compilar]] una versión siguiendo la documentación de abinit.
+=== NetCDF ===
+Una vez que compilamos HDF5 como está indicado en la doc de ABINIT ([[hd|ver instrucciones]]) debemos proceder con NetCDF.
+<code>
+wget https://downloads.unidata.ucar.edu/netcdf-c/4.9.3/netcdf-c-4.9.3.tar.gz
+tar xvf netcdf-c-4.9.3.tar.gz
+wget https://downloads.unidata.ucar.edu/netcdf-fortran/4.6.2/netcdf-fortran-4.6.2.tar.gz
+tar xvf netcdf-fortran-4.6.2.tar.gz
+</code>
+== NetCDF-C ==
+<code>
+./configure --disable-dap --prefix=/data/shared/apps/abinit/10.6.3/libs \
+CC=mpicc \
+LDFLAGS=-L/data/shared/apps/abinit/10.6.3/libs/lib \
+CPPFLAGS=-I/data/shared/apps/abinit/10.6.3/libs/include
+</code>
+Output:
+<code>
+NetCDF C Configuration Summary
+==============================
+# General
+-------
+NetCDF Version:		4.9.3
+Dispatch Version:       5
+Configured On:		Wed Feb 11 18:21:30 -03 2026
+Host System:		x86_64-pc-linux-gnu
+Build Directory: 	/data/shared/apps/abinit/10.6.3/netcdf/netcdf-c-4.9.3
+Install Prefix:         /data/shared/apps/abinit/10.6.3/libs
+# Compiling Options
+-----------------
+C Compiler:		/opt/ohpc/pub/mpi/openmpi5-intel/5.0.3/bin/mpicc
+CFLAGS:			 -fno-strict-aliasing
+CPPFLAGS:		-I/data/shared/apps/abinit/10.6.3/libs/include
+LDFLAGS:		-L/data/shared/apps/abinit/10.6.3/libs/lib
+AM_CFLAGS:
+AM_CPPFLAGS:
+AM_LDFLAGS:
+Shared Library:		yes
+Static Library:		yes
+Extra libraries:	-lhdf5_hl -lhdf5 -lm -lz -lbz2 -lzstd -lxml2
+XML Parser:             libxml2
+Legacy Macros:          yes
+# Features
+--------
+Benchmarks:		no
+NetCDF-2 API:		yes
+HDF4 Support:		no
+HDF5 Support:		yes
+CDF5 Support:		yes
+NC-4 Parallel Support:	yes
+PnetCDF Support:	no
+DAP2 Support:		no
+DAP4 Support:		no
+Byte-Range Support:	no
+S3 Support:	        no
+S3 SDK:  	        none
+NCZarr Support:		yes
+NCZarr Zip Support:     no
+Diskless Support:	yes
+MMap Support:		no
+ERANGE Fill Support:	no
+Relaxed Boundary Check:	yes
+Plugins Enabled:        yes
+Plugin Install Dir:     /data/shared/apps/abinit/10.6.3/libs/hdf5/lib/plugin
+Plugin Search Path:     /data/shared/apps/abinit/10.6.3/libs/hdf5/lib/plugin:/usr/local/hdf5/lib/plugin
+Quantization:		yes
+Logging:     		no
+SZIP Write Support:     no
+Standard Filters:       bz2 deflate zstd
+ZSTD Support:           yes
+Parallel Filters:       yes
+</code>
+Make:
+<code>
+make -j2
+make install
+</code>
+Disclaimer, al hacer make test fallan algunos tests:
+<code>
+FAIL: tst_netcdf4.sh
+FAIL: tst_ncgen4.sh
+FAIL: run_back_comp_tests.sh
+FAIL: tst_nccopy4.sh
+</code>
+Habría que revisar porqué fallan.
+== NetCFD-Fortran ==
+<code>./configure \
+--disable-dap  \
+--prefix=/data/shared/apps/abinit/10.6.3/libs \
+FC=mpifort \
+LDFLAGS=-L/data/shared/apps/abinit/10.6.3/libs/lib \
+FCFLAGS=-I/data/shared/apps/abinit/10.6.3/libs/include
+</code>
+El output debería terminar con:
+<code>
+# NetCDF Fortran Configuration Summary
+==============================
+# General
+-------
+Library Version:                4.6.2
+Configured On:                  Thu Feb 12 11:48:05 -03 2026
+Host System:                    x86_64-pc-linux-gnu
+Build Directory:                /data/shared/apps/abinit/10.6.3/netcdf/netcdf-fortran-4.6.2
+Install Prefix:                 /data/shared/apps/abinit/10.6.3/libs
+# Compiling Options
+-----------------
+Fortran Compiler:               /opt/ohpc/pub/mpi/openmpi5-intel/5.0.3/bin/mpifort
+FFLAGS:                         -g -fallow-argument-mismatch -mismatch_all
+LDFLAGS:                        -L/data/shared/apps/abinit/10.6.3/libs/lib -Wl,-rpath,/data/shared/apps/abinit/10.6.3/libs/lib
+C Compiler:                     /opt/ohpc/pub/mpi/openmpi5-intel/5.0.3/bin/mpicc
+CPPFLAGS:                       -I/data/shared/apps/abinit/10.6.3/libs/include
+CFLAGS:                         -O2 -DLONGLONG_IS_LONG
+Shared Library:                 yes
+Static Library:                 yes
+Extra libraries:                -lnetcdf -lm
+# Features
+--------
+F03:                            yes
+Dap Support:                    no
+Logging Support:                no
+NetCDF-2 API:                   yes
+NetCDF-4 API:                   yes
+CDF5 Support:                   yes
+Parallel IO:                    yes
+NetCDF4 Parallel IO:            yes
+PnetCDF Parallel IO:            no
+SZIP Write Support:             no
+Zstandard Support:              no
+Quantize:                       yes
+configure: WARNING:
+configure: WARNING: ------------------------------------------
+configure: WARNING: libnetcdf was built with zstd support, but HDF5_PLUGIN_PATH is not set, so zstd support is not enabled in libnetcdff. Set HDF5_PLUGIN_PATH and re-run configure if you want to enable zstd support.
+configure: WARNING: You can use `nc-config --plugindir` to determine the appropriate value for HDF5_PLUGIN_PATH
+configure: WARNING: ------------------------------------------
+configure: WARNING:
+</code>
+=== LIBXC ===
+Las implementaciones de libxc de CXXI no fueron compiladas con derivadas terceras:
+<code>
+        +--------------------------------------------------------------+
+        | Suboptimal libxc configuration                               |
+        +--------------------------------------------------------------+
+        | The LibXC package does not provide the 3rd derivatives of    |
+        | energy!                                                      |
+        | You should recompile it using --enable-kxc configure option. |
+        | Otherwise Abinit will not be able to provide nonlinear       |
+        | response properties (Raman intensities, ...).                |
+        +--------------------------------------------------------------+
+</code>
+Vamos a compilarlo específicamente para hacer esto dentro del directorio /data/shared/apps/abinit/<version>/libxc.
+Ver [[libxc|Compilación LibXC 6.2.2]]
+=== Wannier90 ===
+Es necesario agregar un symbolic link
+<code>ln -s libwannier.a libwannier90.a
+</code>
+en el directorio lib/libs.
+== Compilando ==
+Usamos el siguiente archivo de configuración:
+<code snmgt01.ac9>
+prefix="/data/shared/apps/abinit/10.6.3/build"
+CC="icx"
+CXX="mpicxx"
+FC="mpifort"
+with_mpi="/opt/ohpc/pub/mpi/openmpi5-intel/5.0.3"
+with_mpi_flavor="native"
+enable_mpi_gpu_aware="no"
+enable_mpi_inplace="yes"
+enable_mpi_io="auto"
+with_mpi_level="2"
+with_linalg_flavor="mkl"
+LINALG_CPPFLAGS="-I${MKLROOT}/include"
+LINALG_FCFLAGS="-I${MKLROOT}/include"
+LINALG_LIBS="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm -ldl"
+with_fft_flavor="dfti"
+FFT_CPPFLAGS="-I${MKLROOT}/include"
+FFT_FCFLAGS="-I${MKLROOT}/include"
+FFT_LIBS="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm -ldl"
+with_libxc="/data/shared/apps/abinit/10.6.3/libs"
+#LIBXC_LIBS="-L/data/shared/apps/libxc/7.0.0/lib -lxcf90 -lxc"
+#with_libxml2="/data/shared/apps/abinit/10.6.3/tmp/fb"
+with_hdf5="/data/shared/apps/abinit/10.6.3/libs"
+#HDF5_CPPFLAGS="-I/data/shared/apps/abinit/libs/include"
+with_netcdf_fortran="/data/shared/apps/abinit/10.6.3/libs"
+with_netcdf_c="/data/shared/apps/abinit/10.6.3/libs"
+with_wannier90="/data/shared/apps/abinit/10.6.3/libs"
+WANNIER90_LIBS="-L/data/shared/apps/abinit/10.6.3/libs/libi -lwannier -qmkl=sequential"
+with_python_includes="-I/home/bbruzzo/.local/share/mamba/envs/myenv/include/python3.10"
+with_python_libs="-L/home/bbruzzo/.local/share/mamba/envs/myenv/lib -lpython3.10"
+PYTHON_CPPFLAGS="-I/home/bbruzzo/.local/share/mamba/envs/myenv/include/python3.10"
+PYTHON_CFLAGS="-O2"
+PYTHON_LDFLAGS="-L/home/bbruzzo/.local/share/mamba/envs/myenv/lib -lpython3.10"
+</code>
+<code>
+make check
+make test_fast
+make test_in
+make install
+</code>
+== Módulo ==
+<file lua 10.6.3.lua>
+p([==[
+Description
+===========
+ABINIT
+Version
+=======
+.6.3
+More information
+================
+ - Homepage: https://www.abinit.org/
+]==])
+whatis([==[Description:  ABINIT is a software suite to calculate
+the optical, mechanical, vibrational, and other observable
+properties of materials.
+Starting from the quantum equations of density functional theory,
+you can build up to advanced applications with perturbation theories
+based on DFT, and many-body Green's functions (GW and DMFT).
+]==])
+whatis([==[Homepage: https://www.abinit.org]==])
+whatis("Compiled by bbruzzo")
+local root = "/data/shared/apps/abinit/10.6.3/build"
+local libs = "/data/shared/apps/abinit/10.6.3/libs"
+if not ( isloaded("intel/2024.0.0") ) then
+    load("intel/2024.0.0")
+end
+if not ( isloaded("openmpi5") ) then
+    load("openmpi5")
+end
+prepend_path("PATH", pathJoin(root, "/bin"))
+prepend_path("LD_LIBRARY_PATH", pathJoin(libs, "/lib"))
+</file>
+== Check linkeo ==
+<code>
+module purge
+module load abinit
+ldd $(which abinit)
+</code>