3
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I am trying to install Quantum ESPRESSO on a cluster running on CentOS 7. I do not have admin privilege on this cluster.

The compilation with make always exits with the following error even though the ./configure script runs properly. Below is the error I am facing.

[amuhaymin@celestia q-e]$ ./configure
directory QEHeat/src : ok okkokCI : ok
directory ACFDT/src : not present in /home/amuhaymin/opt/q-e/install
directory KCW/PP : okk
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 for gfortran... gfortran
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 the compiler supports GNU Fortran... yes
checking whether gfortran accepts -g... yes
checking for Fortran flag to compile .f90 files... none
checking for mpiifort... no
checking for mpif90... mpif90
checking whether the compiler supports GNU Fortran... yes
checking whether mpif90 accepts -g... yes
checking version of mpif90... gfortran 8.3
setting F90... gfortran
setting MPIF90... mpif90
checking for cc... cc
checking whether the compiler supports GNU C... yes
checking whether cc accepts -g... yes
checking for cc option to enable C11 features... -std=gnu11
setting CC... cc -std=gnu11
setting CFLAGS... -O3
using F90... gfortran
setting FFLAGS... -O3 -g
setting F90FLAGS... $(FFLAGS) -cpp
setting FFLAGS_NOOPT... -O0 -g
setting CPP... cpp
setting CPPFLAGS... -P -traditional -Uvector
setting LD... mpif90
setting LDFLAGS... -g
checking whether make sets $(MAKE)... yes
checking whether Fortran files must be preprocessed... no
checking for library containing dgemm... no
MKL not found
in /opt/intel/mkl/lib/intel64: checking for library containing dgemm... -lmkl_gf_lp64
setting BLAS_LIBS... -L/opt/intel/mkl/lib/intel64 -lmkl_gf_lp64 -lmkl_sequential -lmkl_core
checking FFT...
checking MASS...
checking for library containing mpi_init... none required
checking for library containing pdgemr2d... no
checking for library containing pdgemr2d... -lmkl_scalapack_lp64
checking ELPA...
checking for Environ... not used
checking if legacy plugins are enabled ...  no
checking for ranlib... ranlib
checking for wget... wget -O
setting WGET... wget -O
checking for git... git
Source files are cloned from a git repository.
On git branch develop
On git commit hash 10d110b214ce4b2a5dd1adcc8110feae2f8c5d46
Submodule 'external/d3q' (https://github.com/anharmonic/d3q.git) registered for path 'external/d3q'
Submodule 'external/devxlib' (https://gitlab.com/max-centre/components/devicexlib.git) registered for path 'external/devxlib'
Submodule 'external/fox' (https://github.com/pietrodelugas/fox.git) registered for path 'external/fox'
Submodule 'external/lapack' (https://github.com/Reference-LAPACK/lapack.git) registered for path 'external/lapack'
Submodule 'external/mbd' (https://github.com/libmbd/libmbd.git) registered for path 'external/mbd'
Submodule 'external/pw2qmcpack' (https://github.com/QMCPACK/pw2qmcpack.git) registered for path 'external/pw2qmcpack'
Submodule 'external/qe-gipaw' (https://github.com/dceresoli/qe-gipaw) registered for path 'external/qe-gipaw'
Submodule 'external/wannier90' (https://github.com/wannier-developers/wannier90.git) registered for path 'external/wannier90'
setting DFLAGS... -D__DFTI -D__MPI -D__SCALAPACK
setting IFLAGS... -I. -I$(TOPDIR)/include -I/opt/intel/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
config.status: creating include/qe_cdefs.h
--------------------------------------------------------------------
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=-L/opt/intel/mkl/lib/intel64 -lmkl_gf_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
[amuhaymin@celestia q-e]$ ll
total 212
drwxr-xr-x  2 amuhaymin hpcusers    53 Sep 19 06:25 archive
drwxr-xr-x  6 amuhaymin hpcusers   168 Sep 19 06:25 atomic
drwxr-xr-x  3 amuhaymin hpcusers  4096 Sep 19 06:25 cmake
-rw-r--r--  1 amuhaymin hpcusers 29184 Sep 19 06:25 CMakeLists.txt
-rwxr-xr-x  1 amuhaymin hpcusers  2371 Sep 19 06:25 configure
-rw-r--r--  1 amuhaymin hpcusers  1108 Sep 19 06:25 CONTRIBUTING.md
drwxr-xr-x  6 amuhaymin hpcusers   145 Sep 19 06:25 COUPLE
drwxr-xr-x  6 amuhaymin hpcusers   109 Sep 19 06:25 CPV
drwxr-xr-x  4 amuhaymin hpcusers  4096 Sep 19 06:25 dev-tools
drwxr-xr-x  2 amuhaymin hpcusers   200 Sep 19 06:25 dft-d3
drwxr-xr-x  4 amuhaymin hpcusers  4096 Sep 19 06:25 Doc
-rw-r--r--  1 amuhaymin hpcusers  5274 Sep 19 06:25 environment_variables
drwxr-xr-x  7 amuhaymin hpcusers   168 Sep 19 06:25 EPW
drwxr-xr-x 10 amuhaymin hpcusers  4096 Sep 19 06:25 external
drwxr-xr-x  5 amuhaymin hpcusers   101 Sep 19 06:25 FFTXlib
drwxr-xr-x  5 amuhaymin hpcusers   127 Sep 19 06:25 GUI
drwxr-xr-x 13 amuhaymin hpcusers   251 Sep 19 06:25 GWW
drwxr-xr-x  5 amuhaymin hpcusers   106 Sep 19 06:25 HP
drwxr-xr-x  2 amuhaymin hpcusers   186 Sep 19 06:25 include
drwxr-xr-x  3 amuhaymin hpcusers  4096 Sep 19 06:25 install
drwxr-xr-x  6 amuhaymin hpcusers   138 Sep 19 06:25 KCW
drwxr-xr-x  9 amuhaymin hpcusers   212 Sep 19 06:25 KS_Solvers
drwxr-xr-x  3 amuhaymin hpcusers  4096 Sep 19 06:25 LAXlib
-rw-r--r--  1 amuhaymin hpcusers 18009 Sep 19 06:25 License
-rw-r--r--  1 amuhaymin hpcusers 42741 Sep 19 06:25 logo.jpg
drwxr-xr-x  2 amuhaymin hpcusers  4096 Sep 19 06:25 LR_Modules
-rw-r--r--  1 amuhaymin hpcusers 12344 Sep 19 06:25 Makefile
-rw-r--r--  1 amuhaymin hpcusers  6236 Sep 19 06:25 make.inc
drwxr-xr-x  2 amuhaymin hpcusers  8192 Sep 19 06:25 Modules
drwxr-xr-x  6 amuhaymin hpcusers    95 Sep 19 06:25 NEB
drwxr-xr-x  8 amuhaymin hpcusers   131 Sep 19 06:25 PHonon
drwxr-xr-x  7 amuhaymin hpcusers   151 Sep 19 06:25 PP
drwxr-xr-x  2 amuhaymin hpcusers  4096 Sep 19 06:25 pseudo
drwxr-xr-x  7 amuhaymin hpcusers   158 Sep 19 06:25 PW
drwxr-xr-x  5 amuhaymin hpcusers    82 Sep 19 06:25 PWCOND
drwxr-xr-x  5 amuhaymin hpcusers   124 Sep 19 06:25 QEHeat
-rw-r--r--  1 amuhaymin hpcusers  2880 Sep 19 06:25 README_GPU.md
-rw-r--r--  1 amuhaymin hpcusers  4367 Sep 19 06:25 README.md
drwxr-xr-x  6 amuhaymin hpcusers   176 Sep 19 06:25 TDDFPT
drwxr-xr-x 96 amuhaymin hpcusers  4096 Sep 19 06:25 test-suite
drwxr-xr-x  2 amuhaymin hpcusers  4096 Sep 19 06:25 upflib
drwxr-xr-x  3 amuhaymin hpcusers  4096 Sep 19 06:25 UtilXlib
drwxr-xr-x  4 amuhaymin hpcusers  4096 Sep 19 06:25 XClib
drwxr-xr-x  6 amuhaymin hpcusers   109 Sep 19 06:25 XSpectra
[amuhaymin@celestia q-e]$ make pw
test -d bin || mkdir bin
( cd UtilXlib ; make TLDEPS= all || exit 1 )
make[1]: Entering directory `/home/amuhaymin/opt/q-e/UtilXlib'
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c parallel_include.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c util_param.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c clib_wrappers.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c nvtx_wrapper.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c clocks_handler.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
cc -std=gnu11 -O3 -D__DFTI -D__MPI -D__SCALAPACK -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include   -c cptimer.c
cc -std=gnu11 -O3 -D__DFTI -D__MPI -D__SCALAPACK -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include   -c copy.c
cc -std=gnu11 -O3 -D__DFTI -D__MPI -D__SCALAPACK -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include   -c c_mkdir.c
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c device_helper.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c mp.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c divide.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c data_buffer.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
cc -std=gnu11 -O3 -D__DFTI -D__MPI -D__SCALAPACK -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include   -c eval_infix.c
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c error_handler.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c mp_bands_util.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c export_gstart_2_solvers.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c find_free_unit.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c fletcher32_mod.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
cc -std=gnu11 -O3 -D__DFTI -D__MPI -D__SCALAPACK -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include   -c fletcher32.c
cc -std=gnu11 -O3 -D__DFTI -D__MPI -D__SCALAPACK -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include   -c md5.c
cc -std=gnu11 -O3 -D__DFTI -D__MPI -D__SCALAPACK -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include   -c md5_from_file.c
cc -std=gnu11 -O3 -D__DFTI -D__MPI -D__SCALAPACK -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include   -c memstat.c
cc -std=gnu11 -O3 -D__DFTI -D__MPI -D__SCALAPACK -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include   -c memusage.c
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c mem_counter.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c mp_base.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c mp_base_gpu.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c print_mem.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
cc -std=gnu11 -O3 -D__DFTI -D__MPI -D__SCALAPACK -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include   -c ptrace.c
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c set_mpi_comm_4_solvers.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK  -I/home/amuhaymin/opt/q-e//external/devxlib/src -I. -I/home/amuhaymin/opt/q-e//include -I/opt/intel/mkl/include -I. -c thread_util.f90
f951: Warning: Nonexistent include directory ‘/home/amuhaymin/opt/q-e//external/devxlib/src’ [-Wmissing-include-dirs]
ar ruv libutil.a clib_wrappers.o clocks_handler.o cptimer.o copy.o c_mkdir.o device_helper.o divide.o data_buffer.o eval_infix.o error_handler.o export_gstart_2_solvers.o find_free_unit.o fletcher32_mod.o fletcher32.o md5.o md5_from_file.o memstat.o memusage.o mem_counter.o mp.o mp_base.o mp_base_gpu.o mp_bands_util.o parallel_include.o print_mem.o ptrace.o set_mpi_comm_4_solvers.o util_param.o thread_util.o nvtx_wrapper.o
ar: creating libutil.a
a - clib_wrappers.o
a - clocks_handler.o
a - cptimer.o
a - copy.o
a - c_mkdir.o
a - device_helper.o
a - divide.o
a - data_buffer.o
a - eval_infix.o
a - error_handler.o
a - export_gstart_2_solvers.o
a - find_free_unit.o
a - fletcher32_mod.o
a - fletcher32.o
a - md5.o
a - md5_from_file.o
a - memstat.o
a - memusage.o
a - mem_counter.o
a - mp.o
a - mp_base.o
a - mp_base_gpu.o
a - mp_bands_util.o
a - parallel_include.o
a - print_mem.o
a - ptrace.o
a - set_mpi_comm_4_solvers.o
a - util_param.o
a - thread_util.o
a - nvtx_wrapper.o
ranlib libutil.a
make[1]: Leaving directory `/home/amuhaymin/opt/q-e/UtilXlib'
cd install ; make -f extlibs_makefile libcuda
make[1]: Entering directory `/home/amuhaymin/opt/q-e/install'
initializing external/devxlib submodule ...
usage: git submodule [--quiet] add [-b <branch>] [-f|--force] [--name <name>] [--reference <repository>] [--] <repository> [<path>]
   or: git submodule [--quiet] status [--cached] [--recursive] [--] [<path>...]
   or: git submodule [--quiet] init [--] [<path>...]
   or: git submodule [--quiet] deinit [-f|--force] [--] <path>...
   or: git submodule [--quiet] update [--init] [--remote] [-N|--no-fetch] [-f|--force] [--rebase] [--reference <repository>] [--merge] [--recursive] [--] [<path>...]
   or: git submodule [--quiet] summary [--cached|--files] [--summary-limit <n>] [commit] [--] [<path>...]
   or: git submodule [--quiet] foreach [--recursive] <command>
   or: git submodule [--quiet] sync [--recursive] [--] [<path>...]
make[1]: *** [libcuda_devxlib] Error 1
make[1]: Leaving directory `/home/amuhaymin/opt/q-e/install'
make: *** [libcuda] Error 2

It looks like it cannot find libcuda. But I am not sure if we need libcuda here since this is not GPU!

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1 Answer 1

2
$\begingroup$

If you have root access, make sure you have enabled Fedora EPEL on your system, and then run

# dnf -y install quantum-espresso

If you don't have root access, you should ask your systems administrator to install this package for you.

Alternatively, you can download the necessary RPM packages from Fedora EPEL and extract them with rpm2cpio foo.rpm | cpio -ivd. You will then need to set up your paths and LD_LIBRARY_PATH accordingly, so that the shell finds the necessary binaries and libraries. I often use this trick to install libraries on supercomputers I don't want to bother compiling.

$\endgroup$
5
  • 1
    $\begingroup$ You answered the question in the title, but this doesn't help me actually. I am trying to compile it from the source. That's where the problem is. And since I don't have root access to the cluster, I cannot install anything using dnf. $\endgroup$ Sep 19, 2023 at 14:54
  • 1
    $\begingroup$ Next time be more specific; I answered the question in the title and the description: "I am trying to install Quantum ESPRESSO on a cluster running on CentOS 7." I have changed the title to be more descriptive. $\endgroup$ Sep 19, 2023 at 17:58
  • 4
    $\begingroup$ The original question said "Note that I do not have admin privilege on this cluster", can he still run that dnf command? Also, why would he want to install it with CUDA support if he doesn't have a GPU? $\endgroup$ Sep 20, 2023 at 2:55
  • $\begingroup$ @NikeDattani I have amended the answer. The question was not posed logically which is why I missed some of the details. $\endgroup$ Sep 20, 2023 at 19:07
  • $\begingroup$ I have also reorganized the question to make it clearer. $\endgroup$ Sep 20, 2023 at 19:08

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