[QE-users] users Digest, Vol 203, Issue 22
sjang at sejong.edu
sjang at sejong.edu
Mon Jul 1 15:44:09 CEST 2024
I was able to install using nvc instead of nvcc.
Thanks all for the help. However, all tests are failed giving following
messages.
...
...
pw_workflow_vc-relax_scf - vc-relax-scf-2.in (arg(s): 2): **FAILED**.
Different sets of data extracted from benchmark and test.
Data only in benchmark: n1, e1, band, ef1.
All done. ERROR: only 0 out of 247 tests passed.
Failed tests in:
/home/sjang/install/qe-7.3.1/test-suite/pw_atom/
/home/sjang/install/qe-7.3.1/test-suite/pw_b3lyp/
/home/sjang/install/qe-7.3.1/test-suite/pw_berry/
Thank you again.
SJ
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Today's Topics:
1. input file format for ibrav2cell.x (Bhargab Kakati)
2. Re: input file format for ibrav2cell.x (Paolo Giannozzi)
3. QE installation error with gpu (sjang at sejong.edu)
4. Re: QE installation error with gpu (Paolo Giannozzi)
5. Re: QE installation error with gpu (Pietro Davide Delugas)
6. Input File Verification for Hydrogen Bond Analysis in QE
(Le, Tran T.)
----------------------------------------------------------------------
Message: 1
Date: Fri, 28 Jun 2024 16:41:07 +0530
From: Bhargab Kakati <bhrgabkakati at iasst.res.in>
To: users at lists.quantum-espresso.org
Subject: [QE-users] input file format for ibrav2cell.x
Message-ID: <390ffb834cf77a75ea6180a5b58c3f30 at iasst.res.in>
Content-Type: text/plain; charset=US-ASCII; format=flowed
hello experts,
I want to convert my system parameters so that I can put it in wannier90.win
file . I am trying to use ibrav2cell.x (./ibrav2cell.x <ibrav2cell.in>
ibrav2cell.out) but encountering this error :
"FIO-F-229/namelist read/unit=5/end of file reached while processing group.
File name = 'stdin ', formatted, sequential access record = 5
In source file ibrav2cell.f90, at line number 28 "
my input file was:
" &SYSTEM
ibrav = 7
celldm(1)=7.5872504
celldm(3)=1.8386"
What is the correct format of the input? and what am I doing wrong here?
Any help would be highly appreciated.
Thank You.
------------------------------
Message: 2
Date: Fri, 28 Jun 2024 13:17:20 +0200
From: Paolo Giannozzi <paolo.giannozzi at uniud.it>
To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] input file format for ibrav2cell.x
Message-ID: <abba67c9-889e-412d-8040-e6eb050a5661 at uniud.it>
Content-Type: text/plain; charset=UTF-8; format=flowed
On 6/28/24 13:11, Bhargab Kakati wrote:
> " &SYSTEM
> ?ibrav = 7
> ?celldm(1)=7.5872504
> ?celldm(3)=1.8386"
Namelists must be terminated by a "/" character
Paolo
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ.
Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216 X SCUOLA
ESTIVA DI ENERGIE RINNOVABILI https://scuola-rinnovabili.uniud.it/
------------------------------
Message: 3
Date: Fri, 28 Jun 2024 23:18:51 +0900
From: <sjang at sejong.edu>
To: <users at lists.quantum-espresso.org>
Subject: [QE-users] QE installation error with gpu
Message-ID: <002601dac966$1be21720$53a64560$@sejong.edu>
Content-Type: text/plain; charset="us-ascii"
Hi all,
I am new to QE. I am trying to install QE with GPU. I installed nvidia
hpc_sdk v.24.5 for this on
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5
My gpu is Geforce RTX 3080 (Ampere architecture I suppose).
After successful (?) configure command, I made "make all" and I got
following error.
To me, it seems nvcc compiler doesn't take '-gpu=cc80,cuda12.4' option.
In fact,
$ which nvcc
/opt/nvidia/hpc_sdk/Linux_x86_64/2024/cuda/12.4/bin/nvcc
$ nvcc -gpu=cc80,cuda12.4
nvcc fatal : Unknown option '-gpu=cc80,cuda12.4'
I might be wrong though.
Any advice or help will be greatly apprecited.
Thank you very much in advance.
SJ
$make all
make[1]: Entering directory `/home/sjang/install/qe-7.3.1/UtilXlib'
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -D__PGI -D__CUDA
-D__DFTI -D__MPI -D__SCALAPACK -cuda -gpu=cc80,cuda12.4
-I/home/sjang/install/qe-7.3.1//external/devxlib/src
-I/home/sjang/install/qe-7.3.1//external/devxlib/include -acc
-I/home/sjang/install/qe-7.3.1//external/devxlib/src -I.
-I/home/sjang/install/qe-7.3.1//include
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include -I.
-c parallel_include.f90
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -D__PGI -D__CUDA
-D__DFTI -D__MPI -D__SCALAPACK -cuda -gpu=cc80,cuda12.4
-I/home/sjang/install/qe-7.3.1//external/devxlib/src
-I/home/sjang/install/qe-7.3.1//external/devxlib/include -acc
-I/home/sjang/install/qe-7.3.1//external/devxlib/src -I.
-I/home/sjang/install/qe-7.3.1//include
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include -I.
-c util_param.f90
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -D__PGI -D__CUDA
-D__DFTI -D__MPI -D__SCALAPACK -cuda -gpu=cc80,cuda12.4
-I/home/sjang/install/qe-7.3.1//external/devxlib/src
-I/home/sjang/install/qe-7.3.1//external/devxlib/include -acc
-I/home/sjang/install/qe-7.3.1//external/devxlib/src -I.
-I/home/sjang/install/qe-7.3.1//include
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include -I.
-c clib_wrappers.f90
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -D__PGI -D__CUDA
-D__DFTI -D__MPI -D__SCALAPACK -cuda -gpu=cc80,cuda12.4
-I/home/sjang/install/qe-7.3.1//external/devxlib/src
-I/home/sjang/install/qe-7.3.1//external/devxlib/include -acc
-I/home/sjang/install/qe-7.3.1//external/devxlib/src -I.
-I/home/sjang/install/qe-7.3.1//include
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include -I.
-c nvtx_wrapper.f90
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -D__PGI -D__CUDA
-D__DFTI -D__MPI -D__SCALAPACK -cuda -gpu=cc80,cuda12.4
-I/home/sjang/install/qe-7.3.1//external/devxlib/src
-I/home/sjang/install/qe-7.3.1//external/devxlib/include -acc
-I/home/sjang/install/qe-7.3.1//external/devxlib/src -I.
-I/home/sjang/install/qe-7.3.1//include
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include -I.
-c clocks_handler.f90
nvcc -O3 -D__PGI -D__CUDA -D__DFTI -D__MPI -D__SCALAPACK -I.
-I/home/sjang/install/qe-7.3.1//include
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include
-gpu=cc80,cuda12.4 -acc -c cptimer.c
nvcc fatal : Unknown option '-gpu=cc80,cuda12.4'
make[1]: *** [cptimer.o] Error 1
make[1]: Leaving directory `/home/sjang/install/qe-7.3.1/UtilXlib'
make: *** [libutil] Error 1
----------------------------------------------------------------------------
----------------------
Before 'make all' command, this is my configure command and resulting log
$echo $NVHPC_CUDA_HOME
/opt/nvidia/hpc_sdk/Linux_x86_64/2024/cuda/12.4
$./configure F90=nvfortran
MPIF90=/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi
-4.1.5/bin/mpif90 CC=nvcc CXX=nvc++ --with-cuda=$NVHPC_CUDA_HOME
--prefix=$HOME/QE --with-cuda-cc=80 --with-cuda-runtime=12.4
..
..
all dependencies updated successfully
checking build system type... x86_64-pc-linux-gnu
checking ARCH... x86_64
checking setting AR... ... ar
checking setting ARFLAGS... ... ruv
checking whether the Fortran compiler works... yes
checking for Fortran compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU Fortran compiler... no
checking whether
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/compilers/bin/nvfortran accepts -g...
yes
checking for Fortran flag to compile .f90 files... none
checking for
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90... no
checking whether we are using the GNU Fortran compiler... no
checking whether accepts -g... no
configure: WARNING: MPIF90 not found: using MPIF90 anyway
checking version of
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90... nvfortran 24.5-1
configure: WARNING: Check whether user-supplied F90 is consistent with
MPIF90 !!!
setting F90... nvfortran
setting MPIF90...
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90
checking whether we are using the GNU C compiler... yes
checking whether nvcc accepts -g... yes
checking for nvcc option to accept ISO C89... none needed
setting CC... nvcc
setting CFLAGS... -O3
using F90... nvfortran
setting FFLAGS... -fast
setting F90FLAGS... -fast -Mcache_align -Mpreprocess -Mlarge_arrays
setting FFLAGS_NOOPT... -O0
setting FFLAGS_NOMAIN... -Mnomain
setting CPP... cpp
setting CPPFLAGS... -P -traditional -Uvector
setting LD...
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90
setting LDFLAGS...
checking whether Fortran compiler accepts -cuda -gpu=cuda12.4... yes
checking whether make sets $(MAKE)... yes
checking whether Fortran files must be preprocessed... no
checking for library containing dgemm... -lmkl_intel_lp64
setting BLAS_LIBS... -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
checking FFT...
checking MASS...
checking for library containing mpi_init... none required
checking for library containing pdgemr2d... no
checking for library containing pdgemr2d... -lmkl_scalapack_lp64
checking ELPA...
checking for Environ... not used
checking if legacy plugins are enabled ... no
checking for ranlib... ranlib
checking for wget... wget -O
setting WGET... wget -O
checking for git... git
setting DFLAGS... -D__PGI -D__CUDA -D__DFTI -D__MPI -D__SCALAPACK
setting IFLAGS... -I. -I$(TOPDIR)/include
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include
configure: creating ./config.status
config.status: creating install/make_lapack.inc
config.status: creating include/configure.h
config.status: creating make.inc
config.status: creating configure.msg
config.status: creating install/make_wannier90.inc
--------------------------------------------------------------------
ESPRESSO can take advantage of several optimized numerical libraries
(essl, fftw, mkl...). This configure script attempts to find them,
but may fail if they have been installed in non-standard locations.
If a required library is not found, the local copy will be compiled.
The following libraries have been found:
BLAS_LIBS= -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
LAPACK_LIBS=
SCALAPACK_LIBS=-lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64
FFT_LIBS=
Please check if this is what you expect.
If any libraries are missing, you may specify a list of directories
to search and retry, as follows:
./configure LIBDIRS="list of directories, separated by spaces"
Parallel environment detected successfully.\
Configured for compilation of parallel executables.
For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex).
--------------------------------------------------------------------
configure: success
----------------------------------------------------------------------------
----------------------
Here is my PATH info
echo $PATH
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/compilers/extras/qd/bin:/opt/nvidia/hp
c_sdk/Linux_x86_64/24.5/cuda/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/2024/cuda/
12.4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/mpi/bin:/opt/nvidia
/hpc_sdk/Linux_x86_64/24.5/compilers/bin:/home/sjang/software/xdrfile/bin:/h
ome/sjang/software/plumed272_intel/bin:/usr/local/mpi/intel19/openmpi-3.1.6/
bin:/home/sjang/software/GMX2021_plumed272_intel/bin:/home/sjang/vmd/bin:/ho
me/sjang/software/packmol:/home/sjang/software/rosetta_src_2021.16.61629_bun
dle/main/source/bin:/home/sjang/g16/g16/bsd:/home/sjang/g16/g16:/usr/local/i
ntel/compilers_and_libraries_2020.4.304/linux/bin/intel64:/usr/local/intel/c
ompilers_and_libraries_2020.4.304/linux/bin:/usr/local/intel/compilers_and_l
ibraries_2020.4.304/linux/mpi/intel64/libfabric/bin:/usr/local/intel/compile
rs_and_libraries_2020.4.304/linux/mpi/intel64/bin:/usr/local/intel/debugger_
2020/gdb/intel64/bin:/opt/rh/devtoolset-9/root/usr/bin:/usr/local/anaconda/3
/2021.05/bin:/usr/local/anaconda/3/2021.05/condabin:/opt/nvidia/hpc_sdk/Linu
x_x86_64/2024/cuda/12.4/bin:/usr/lib64/qt-3.3/bin:/usr/torque/sbin:/usr/torq
ue/bin:/opt/pbs/sbin:/opt/pbs/bin:/usr/local/jspcmds:.:/home/my_uer_name:/us
r/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin
----------------------------------------------------------------------------
----------------------
Here is my LD_LIBRARY_PATH info
echo $LD_LIBRARY_PATH
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/nvshmem/lib:/opt/nvidia/hpc_
sdk/Linux_x86_64/24.5/comm_libs/nccl/lib:/opt/nvidia/hpc_sdk/Linux_x86_64/24
.5/math_libs/lib64:/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/compilers/lib:/opt/
nvidia/hpc_sdk/Linux_x86_64/24.5/compilers/extras/qd/lib:/opt/nvidia/hpc_sdk
/Linux_x86_64/24.5/cuda/extras/CUPTI/lib64:/opt/nvidia/hpc_sdk/Linux_x86_64/
24.5/cuda/lib64:/opt/nvidia/hpc_sdk/Linux_x86_64/2024/cuda/12.4/extras/CUPTI
/lib64:/opt/nvidia/hpc_sdk/Linux_x86_64/2024/cuda/12.4/lib64:/opt/nvidia/hpc
_sdk/Linux_x86_64/24.5/math_libs:/usr/local/lib:/home/sjang/software/xdrfile
/lib:/home/sjang/software/plumed272_intel/lib:/usr/local/mpi/intel19/openmpi
-3.1.6/lib:/usr/local/intel/compilers_and_libraries_2020.4.304/linux/compile
r/lib/intel64_lin:/usr/local/intel/compilers_and_libraries_2020.4.304/linux/
mpi/intel64/libfabric/lib:/usr/local/intel/compilers_and_libraries_2020.4.30
4/linux/mpi/intel64/lib/release:/usr/local/intel/compilers_and_libraries_202
0.4.304/linux/mpi/intel64/lib:/usr/local/intel/compilers_and_libraries_2020.
4.304/linux/ipp/lib/intel64:/usr/local/intel/compilers_and_libraries_2020.4.
304/linux/mkl/lib/intel64_lin:/usr/local/intel/compilers_and_libraries_2020.
4.304/linux/tbb/lib/intel64/gcc4.8:/usr/local/intel/debugger_2020/python/int
el64/lib:/usr/local/intel/debugger_2020/libipt/intel64/lib:/usr/local/intel/
compilers_and_libraries_2020.4.304/linux/daal/lib/intel64_lin:/usr/local/int
el/compilers_and_libraries_2020.4.304/linux/daal/../tbb/lib/intel64_lin/gcc4
.4:/usr/local/intel/compilers_and_libraries_2020.4.304/linux/daal/../tbb/lib
/intel64_lin/gcc4.8:/opt/rh/devtoolset-9/root/usr/lib64:/opt/rh/devtoolset-9
/root/usr/lib:/opt/rh/devtoolset-9/root/usr/lib64/dyninst:/opt/rh/devtoolset
-9/root/usr/lib/dyninst:/opt/nvidia/hpc_sdk/Linux_x86_64/2024/cuda/12.4/extr
as/CUPTI/lib64:/opt/nvidia/hpc_sdk/Linux_x86_64/2024/cuda/12.4/lib64:/home/s
jang/g16/gv/lib
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------------------------------
Message: 4
Date: Fri, 28 Jun 2024 16:57:19 +0200
From: Paolo Giannozzi <paolo.giannozzi at uniud.it>
To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>,
sjang at sejong.edu
Subject: Re: [QE-users] QE installation error with gpu
Message-ID: <a5a71a08-4aaa-4503-8e5d-7186b8bddcce at uniud.it>
Content-Type: text/plain; charset=UTF-8; format=flowed
On 6/28/24 16:18, sjang at sejong.edu wrote:
> After successful (?) configure command, I made "make all" and I got
> following error.
>
> To me, it seems nvcc compiler doesn?t take '-gpu=cc80,cuda12.4' option.
in fact "configure" selects pgcc, not nvcc (don't ask me why). Ensure
that you have NVidia compilers in the path, that OMPI_FC points to
nvfortran, then use "configure" with the needed options only:
$ ./configure --with-cuda=$NVHPC_CUDA_HOME --with-cuda-cc=80
--with-cuda-runtime=12.4 [ --prefix=$HOME/QE if you wish ]
Paolo
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
X SCUOLA ESTIVA DI ENERGIE RINNOVABILI https://scuola-rinnovabili.uniud.it/
------------------------------
Message: 5
Date: Fri, 28 Jun 2024 15:47:56 +0000
From: Pietro Davide Delugas <pdelugas at sissa.it>
To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] QE installation error with gpu
Message-ID: <0289f038-96c9-4782-9f4a-dc943a6187fd at email.android.com>
Content-Type: text/plain; charset="utf-8"
Hello
Try with CC=nvc, nvcc is the cuda compiler
Il 28 giu 2024 4:20?PM, sjang at sejong.edu ha scritto:
Hi all,
I am new to QE. I am trying to install QE with GPU. I installed nvidia
hpc_sdk v.24.5 for this on
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5
My gpu is Geforce RTX 3080 (Ampere architecture I suppose).
After successful (?) configure command, I made "make all" and I got
following error.
To me, it seems nvcc compiler doesn?t take '-gpu=cc80,cuda12.4' option.
In fact,
$ which nvcc
/opt/nvidia/hpc_sdk/Linux_x86_64/2024/cuda/12.4/bin/nvcc
$ nvcc -gpu=cc80,cuda12.4
nvcc fatal : Unknown option '-gpu=cc80,cuda12.4'
I might be wrong though.
Any advice or help will be greatly apprecited.
Thank you very much in advance.
SJ
$make all
make[1]: Entering directory `/home/sjang/install/qe-7.3.1/UtilXlib'
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -D__PGI -D__CUDA
-D__DFTI -D__MPI -D__SCALAPACK -cuda -gpu=cc80,cuda12.4
-I/home/sjang/install/qe-7.3.1//external/devxlib/src
-I/home/sjang/install/qe-7.3.1//external/devxlib/include -acc
-I/home/sjang/install/qe-7.3.1//external/devxlib/src -I.
-I/home/sjang/install/qe-7.3.1//include
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include -I.
-c parallel_include.f90
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -D__PGI -D__CUDA
-D__DFTI -D__MPI -D__SCALAPACK -cuda -gpu=cc80,cuda12.4
-I/home/sjang/install/qe-7.3.1//external/devxlib/src
-I/home/sjang/install/qe-7.3.1//external/devxlib/include -acc
-I/home/sjang/install/qe-7.3.1//external/devxlib/src -I.
-I/home/sjang/install/qe-7.3.1//include
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include -I.
-c util_param.f90
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -D__PGI -D__CUDA
-D__DFTI -D__MPI -D__SCALAPACK -cuda -gpu=cc80,cuda12.4
-I/home/sjang/install/qe-7.3.1//external/devxlib/src
-I/home/sjang/install/qe-7.3.1//external/devxlib/include -acc
-I/home/sjang/install/qe-7.3.1//external/devxlib/src -I.
-I/home/sjang/install/qe-7.3.1//include
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include -I.
-c clib_wrappers.f90
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -D__PGI -D__CUDA
-D__DFTI -D__MPI -D__SCALAPACK -cuda -gpu=cc80,cuda12.4
-I/home/sjang/install/qe-7.3.1//external/devxlib/src
-I/home/sjang/install/qe-7.3.1//external/devxlib/include -acc
-I/home/sjang/install/qe-7.3.1//external/devxlib/src -I.
-I/home/sjang/install/qe-7.3.1//include
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include -I.
-c nvtx_wrapper.f90
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -D__PGI -D__CUDA
-D__DFTI -D__MPI -D__SCALAPACK -cuda -gpu=cc80,cuda12.4
-I/home/sjang/install/qe-7.3.1//external/devxlib/src
-I/home/sjang/install/qe-7.3.1//external/devxlib/include -acc
-I/home/sjang/install/qe-7.3.1//external/devxlib/src -I.
-I/home/sjang/install/qe-7.3.1//include
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include -I.
-c clocks_handler.f90
nvcc -O3 -D__PGI -D__CUDA -D__DFTI -D__MPI -D__SCALAPACK -I.
-I/home/sjang/install/qe-7.3.1//include
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include
-gpu=cc80,cuda12.4 -acc -c cptimer.c
nvcc fatal : Unknown option '-gpu=cc80,cuda12.4'
make[1]: *** [cptimer.o] Error 1
make[1]: Leaving directory `/home/sjang/install/qe-7.3.1/UtilXlib'
make: *** [libutil] Error 1
----------------------------------------------------------------------------
----------------------
Before ?make all? command, this is my configure command and resulting log
$echo $NVHPC_CUDA_HOME
/opt/nvidia/hpc_sdk/Linux_x86_64/2024/cuda/12.4
$./configure F90=nvfortran
MPIF90=/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi
-4.1.5/bin/mpif90 CC=nvcc CXX=nvc++ --with-cuda=$NVHPC_CUDA_HOME
--prefix=$HOME/QE --with-cuda-cc=80 --with-cuda-runtime=12.4
?.
?.
all dependencies updated successfully
checking build system type... x86_64-pc-linux-gnu
checking ARCH... x86_64
checking setting AR... ... ar
checking setting ARFLAGS... ... ruv
checking whether the Fortran compiler works... yes
checking for Fortran compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU Fortran compiler... no
checking whether
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/compilers/bin/nvfortran accepts -g...
yes
checking for Fortran flag to compile .f90 files... none
checking for
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90... no
checking whether we are using the GNU Fortran compiler... no
checking whether accepts -g... no
configure: WARNING: MPIF90 not found: using MPIF90 anyway
checking version of
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90... nvfortran 24.5-1
configure: WARNING: Check whether user-supplied F90 is consistent with
MPIF90 !!!
setting F90... nvfortran
setting MPIF90...
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90
checking whether we are using the GNU C compiler... yes
checking whether nvcc accepts -g... yes
checking for nvcc option to accept ISO C89... none needed
setting CC... nvcc
setting CFLAGS... -O3
using F90... nvfortran
setting FFLAGS... -fast
setting F90FLAGS... -fast -Mcache_align -Mpreprocess -Mlarge_arrays
setting FFLAGS_NOOPT... -O0
setting FFLAGS_NOMAIN... -Mnomain
setting CPP... cpp
setting CPPFLAGS... -P -traditional -Uvector
setting LD...
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/
bin/mpif90
setting LDFLAGS...
checking whether Fortran compiler accepts -cuda -gpu=cuda12.4... yes
checking whether make sets $(MAKE)... yes
checking whether Fortran files must be preprocessed... no
checking for library containing dgemm... -lmkl_intel_lp64
setting BLAS_LIBS... -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
checking FFT...
checking MASS...
checking for library containing mpi_init... none required
checking for library containing pdgemr2d... no
checking for library containing pdgemr2d... -lmkl_scalapack_lp64
checking ELPA...
checking for Environ... not used
checking if legacy plugins are enabled ... no
checking for ranlib... ranlib
checking for wget... wget -O
setting WGET... wget -O
checking for git... git
setting DFLAGS... -D__PGI -D__CUDA -D__DFTI -D__MPI -D__SCALAPACK
setting IFLAGS... -I. -I$(TOPDIR)/include
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include
configure: creating ./config.status
config.status: creating install/make_lapack.inc
config.status: creating include/configure.h
config.status: creating make.inc
config.status: creating configure.msg
config.status: creating install/make_wannier90.inc
--------------------------------------------------------------------
ESPRESSO can take advantage of several optimized numerical libraries
(essl, fftw, mkl...). This configure script attempts to find them,
but may fail if they have been installed in non-standard locations.
If a required library is not found, the local copy will be compiled.
The following libraries have been found:
BLAS_LIBS= -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
LAPACK_LIBS=
SCALAPACK_LIBS=-lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64
FFT_LIBS=
Please check if this is what you expect.
If any libraries are missing, you may specify a list of directories
to search and retry, as follows:
./configure LIBDIRS="list of directories, separated by spaces"
Parallel environment detected successfully.\
Configured for compilation of parallel executables.
For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex).
--------------------------------------------------------------------
configure: success
----------------------------------------------------------------------------
----------------------
Here is my PATH info
echo $PATH
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/compilers/extras/qd/bin:/opt/nvidia/hp
c_sdk/Linux_x86_64/24.5/cuda/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/2024/cuda/
12.4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/mpi/bin:/opt/nvidia
/hpc_sdk/Linux_x86_64/24.5/compilers/bin:/home/sjang/software/xdrfile/bin:/h
ome/sjang/software/plumed272_intel/bin:/usr/local/mpi/intel19/openmpi-3.1.6/
bin:/home/sjang/software/GMX2021_plumed272_intel/bin:/home/sjang/vmd/bin:/ho
me/sjang/software/packmol:/home/sjang/software/rosetta_src_2021.16.61629_bun
dle/main/source/bin:/home/sjang/g16/g16/bsd:/home/sjang/g16/g16:/usr/local/i
ntel/compilers_and_libraries_2020.4.304/linux/bin/intel64:/usr/local/intel/c
ompilers_and_libraries_2020.4.304/linux/bin:/usr/local/intel/compilers_and_l
ibraries_2020.4.304/linux/mpi/intel64/libfabric/bin:/usr/local/intel/compile
rs_and_libraries_2020.4.304/linux/mpi/intel64/bin:/usr/local/intel/debugger_
2020/gdb/intel64/bin:/opt/rh/devtoolset-9/root/usr/bin:/usr/local/anaconda/3
/2021.05/b
in:/usr/local/anaconda/3/2021.05/condabin:/opt/nvidia/hpc_sdk/Linux_x86_64/2
024/cuda/12.4/bin:/usr/lib64/qt-3.3/bin:/usr/torque/sbin:/usr/torque/bin:/op
t/pbs/sbin:/opt/pbs/bin:/usr/local/jspcmds:.:/home/my_uer_name:/usr/local/bi
n:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin
----------------------------------------------------------------------------
----------------------
Here is my LD_LIBRARY_PATH info
echo $LD_LIBRARY_PATH
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/nvshmem/lib:/opt/nvidia/hpc_
sdk/Linux_x86_64/24.5/comm_libs/nccl/lib:/opt/nvidia/hpc_sdk/Linux_x86_64/24
.5/math_libs/lib64:/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/compilers/lib:/opt/
nvidia/hpc_sdk/Linux_x86_64/24.5/compilers/extras/qd/lib:/opt/nvidia/hpc_sdk
/Linux_x86_64/24.5/cuda/extras/CUPTI/lib64:/opt/nvidia/hpc_sdk/Linux_x86_64/
24.5/cuda/lib64:/opt/nvidia/hpc_sdk/Linux_x86_64/2024/cuda/12.4/extras/CUPTI
/lib64:/opt/nvidia/hpc_sdk/Linux_x86_64/2024/cuda/12.4/lib64:/opt/nvidia/hpc
_sdk/Linux_x86_64/24.5/math_libs:/usr/local/lib:/home/sjang/software/xdrfile
/lib:/home/sjang/software/plumed272_intel/lib:/usr/local/mpi/intel19/openmpi
-3.1.6/lib:/usr/local/intel/compilers_and_libraries_2020.4.304/linux/compile
r/lib/intel64_lin:/usr/local/intel/compilers_and_libraries_2020.4.304/linux/
mpi/intel64/libfabric/lib:/usr/local/intel/compilers_and_libraries_2020.4.30
4/linux/mpi/intel64/lib/release:/usr/local/intel/compilers_and_libraries_202
0.4.304/li
nux/mpi/intel64/lib:/usr/local/intel/compilers_and_libraries_2020.4.304/linu
x/ipp/lib/intel64:/usr/local/intel/compilers_and_libraries_2020.4.304/linux/
mkl/lib/intel64_lin:/usr/local/intel/compilers_and_libraries_2020.4.304/linu
x/tbb/lib/intel64/gcc4.8:/usr/local/intel/debugger_2020/python/intel64/lib:/
usr/local/intel/debugger_2020/libipt/intel64/lib:/usr/local/intel/compilers_
and_libraries_2020.4.304/linux/daal/lib/intel64_lin:/usr/local/intel/compile
rs_and_libraries_2020.4.304/linux/daal/../tbb/lib/intel64_lin/gcc4.4:/usr/lo
cal/intel/compilers_and_libraries_2020.4.304/linux/daal/../tbb/lib/intel64_l
in/gcc4.8:/opt/rh/devtoolset-9/root/usr/lib64:/opt/rh/devtoolset-9/root/usr/
lib:/opt/rh/devtoolset-9/root/usr/lib64/dyninst:/opt/rh/devtoolset-9/root/us
r/lib/dyninst:/opt/nvidia/hpc_sdk/Linux_x86_64/2024/cuda/12.4/extras/CUPTI/l
ib64:/opt/nvidia/hpc_sdk/Linux_x86_64/2024/cuda/12.4/lib64:/home/sjang/g16/g
v/lib
-------------- next part --------------
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------------------------------
Message: 6
Date: Fri, 28 Jun 2024 21:57:58 +0000
From: "Le, Tran T." <tran.le.15 at ou.edu>
To: "users at lists.quantum-espresso.org"
<users at lists.quantum-espresso.org>
Subject: [QE-users] Input File Verification for Hydrogen Bond Analysis
in QE
Message-ID:
<SA1PR03MB7053066AC5FAA50F98952156BED02 at SA1PR03MB7053.namprd03.prod.outlook.
com>
Content-Type: text/plain; charset="utf-8"
Dear all,
I have just started using Quantum ESPRESSO as my main research involves
molecular dynamics simulations. I am working on relaxing a system consisting
of a polymer and CO2. I would like to determine if any hydrogen bonds are
formed between them. I was wondering if my input file is correct for this
calculation. Below is my input:
&control
calculation='relax',
restart_mode='from_scratch',
prefix='PPN-CO2',
pseudo_dir = ''
outdir=''
??tprnfor = .true.
/
&system
ibrav= 1,
?celled(1) = 120.0,
? nat = 99,
ntyp = 4,
ecutwfc =50, ecutrho =500,
vdw_corr = grimme-d3,
/
&electrons
conv_thr = 1.0d-8
/
&ions
/
ATOMIC_SPECIES
C 12.0107 C.pbe-rrkjus.UPF
H 1.0 H.pbe-rrkjus.UPF
O 16.0 O.pbe-rrkjus.UPF
N 14.0067 N.pbe-n-rrkjus_psl.1.0.0.UPF
ATOMIC_POSITIONS {angstrom}
H 113.8990785?????-15.39184566??????4.990010336
C 103.6087457?????-13.6607655?7.758425331
C 100.4996082?????-2.791566269??????15.83035089
H 108.2106547?????3.892021952?19.32772387
C????? 87.22710646??????-0.822517358??????19.0637291
N????? 81.33741994??????9.284595346?26.51144201
H????? 86.33487597??????16.87867949?30.87252121
C????? 67.69509919??????8.116687545?27.11960545
O????? 60.35915198??????15.70959919?32.95740402
C????? 63.91231632??????-4.4348188??19.2021683
H????? 58.85285263??????-11.44772753??????25.90482722
C????? 77.25626748??????-9.521485124??????14.54332951
C????? 80.43619681??????-20.18725804??????6.461887946
H????? 72.70211436??????-26.72445293??????2.751164738
C????? 93.77057159??????-22.19799892??????3.092855262
H????? 96.4689941?-30.45844125??????-3.29875257
C????? 55.01160706??????-1.416209211??????7.400638638
C????? 59.65505941??????7.035391748?-2.591173754
H????? 69.26509144??????11.89781924?-1.452144317
C????? 52.28849438??????9.101607835?-14.13269829
H????? 56.03512431??????15.5825958??-21.91430571
C????? 40.21175626??????2.619288713?-15.63259906
C????? 31.27010035??????3.13949672??-27.78759979
H????? 35.1831681?9.417844756?-35.78407974
C????? 17.92789593??????7.756187974?-22.4987659
C????? 12.86740326??????-0.315721609??????-12.31115828
C????? 21.93895883??????-11.84113175??????-8.716171107
H????? 18.01498686??????-18.09918924??????-0.707973384
C????? 35.28772949??????-5.543337325??????-5.456821882
C????? 42.63302669??????-7.609114397??????6.024194344
H????? 38.87612172??????-14.06405815??????13.83034548
C????? 24.34676299??????-19.33264277??????-21.61930542
C????? 22.2487633?-32.80646178??????-23.73645765
H????? 18.41026344??????-39.06955719??????-15.80831752
C????? 25.17177951??????-38.22746829??????-36.1636799
H????? 23.63409299??????-48.77555561??????-37.87193846
C????? 30.11432006??????-30.22918643??????-46.3212561
H????? 32.34822692??????-34.54682446??????-55.92000734
C????? 32.21066525??????-16.67658091??????-44.21425494
C????? 29.36149779??????-11.28942045??????-31.84859619
H????? 36.10792351??????-10.43351394??????-52.1215381
C????? 0.857855927?????2.733821267?-6.310212559
H????? -3.123833929?????-3.424220434??????1.610881915
C????? -6.02778801??????14.19314556?-10.27349379
C????? -0.867838073?????22.26684843?-20.28763975
H????? -6.116842988?????31.22244316?-23.23075254
C????? 11.06700068??????18.99039805?-26.54528841
H????? 14.98993159??????25.30757025?-34.37615987
C?????-18.65518235??????17.88251004?-2.749069955
C?????-13.96982095??????21.57957404?11.4521929
O????? -8.090017259?????14.59615191?19.34770564
N?????-17.1980554?34.67596267?13.52231932
H?????-14.82831874??????39.64208337?21.97199083
C?????-23.92709983??????40.26217323?2.754453607
C?????-29.09418561??????52.97340541?1.291204946
H?????-28.05557402??????60.40579474?9.035134852
C?????-35.7461916?55.89840547?-10.54485225
H?????-39.88123129??????65.76933054?-11.97474714
C?????-37.24737438??????46.36869644?-20.4746696
H?????-42.56149676??????48.86945952?-29.52624392
C?????-31.99252529??????33.59708812?-18.91889655
C?????-25.20087538??????30.66378025?-7.311644091
H?????-33.18661501??????26.12576671?-26.61724105
C?????-29.12426598??????6.957418346?-3.14664998
C?????-37.99830725??????5.329128035?7.4404323
H?????-36.80788099??????11.05900886?16.5183901
C?????-48.31758724??????-3.739186072??????6.281288677
C?????-58.56513939??????-6.870734935??????16.9146146
H?????-57.11353062??????-1.220581882??????26.11950978
C?????-71.99597952??????-4.508618285??????10.44514457
C?????-73.82200379??????-11.74119809??????-1.337690697
C?????-85.71363999??????-10.79843411??????-8.290310409
H?????-87.18426008??????-16.4130564?-17.40592444
C?????-95.78257237??????-2.585413356??????-3.415475963
H?????-105.1425787??????-1.852948051??????-8.770337862
C?????-93.94771862??????4.612357312?8.261996567
H?????-101.861308?10.95288756?11.99120532
C?????-81.99987811??????3.686542355?15.26278701
H?????-80.55861858??????9.271125057?24.40457562
C?????-61.97141639??????-20.34617851??????-5.021678753
H?????-63.42606003??????-25.99275119??????-14.23232632
C?????-50.07981261??????-11.06488417??????-5.451180122
C?????-41.20463747??????-9.584275226??????-15.89981845
H?????-42.39501388??????-15.31585913??????-24.98189693
C?????-30.73548471??????-0.584523586??????-14.69324518
H?????-23.73564173??????0.605870748?-22.82576773
C?????-59.52505156??????-29.08188789??????7.071005071
C?????-58.88276323??????-42.8546198?7.174894336
H?????-60.26312849??????-48.5074867?-1.930181594
C?????-56.41138361??????-49.40697519??????19.1632183
H?????-55.85984572??????-60.19175937??????19.33052423
C?????-54.67707921??????-42.21628209??????30.87122975
H?????-52.80193531??????-47.42120361??????40.13977713
C?????-55.32152337??????-28.35601902??????30.77183577
C?????-57.70323216??????-21.84085427??????18.84989429
H?????-54.01532735??????-22.72248522??????39.88854783
C?????19.6835097??12.52991224?18.55344661
O?????19.77582415?3.647514108?25.73720991
O 19.80329629?????21.41247841?11.32436868
K_POINTS {gamma}
#K_POINTS {gamma}
# 3 3 1 0 0 0
Thank you.
Best regards,
Tran
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------------------------------
Subject: Digest Footer
_______________________________________________
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples.
_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list users at lists.quantum-espresso.org
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------------------------------
End of users Digest, Vol 203, Issue 22
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