Dear Amber Users,
I have worked out and sorted the issue of installation. I realized that our firewall is ON and thereby not allowing ./update_amber script to update the patches.
The following site helped alot to fix the error.
http://jswails.wikidot.com/using-update-amber
Once I granted the access to www.ambermd.org<
http://www.ambermd.org> site, cuda version installation went smoothly and pmemd.cuda passed the test runs.
[
http://ambermd.org/images/amber_mol_fitted.jpg]<
http://www.ambermd.org/>
The Amber Molecular Dynamics Package<
http://www.ambermd.org/>
Welcome to Amber! Amber is a suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active development community; see our history page and our contributors page for more information.. The term "Amber" refers to two things.
www.ambermd.org
Using update_amber - jswails<
http://jswails.wikidot.com/using-update-amber>
This will go online, download any patches that may be available and apply them each one by one. Note: If any updates patch update_amber or any of the modules in updateutils/, it stops applying patches so that future patches can be applied with the fixed version. If this happens, a message will be printed after it quits, describing what to do.
jswails.wikidot.com
Thanks everyone for your time.
Regards,
Kumar
________________________________
From: Nagakumar Bharatham
Sent: 19 November 2020 14:26
To: amber.ambermd.org <amber.ambermd.org>
Subject: Amber 18 GPU installation error
Dear Amber Users/Developers,
I am trying to install Amber 18 on our RTX2080Ti GPU cluster
Here are System and software details
CentoS7.8
Cuda-9.0
Driver Version: 450.80.02
GPU Type: RTX2080Ti
Commands exicuted:
yum -y install tcsh make \
which flex bison patch bc \
libXt-devel libXext-devel \
perl perl-ExtUtils-MakeMaker util-linux wget \
bzip2 bzip2-devel zlib-devel tar
/usr/local/cuda/bin/nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2017 NVIDIA Corporation
Built on Fri_Sep__1_21:08:03_CDT_2017
Cuda compilation tools, release 9.0, V9.0.176
gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-39) (GCC)
-------------------------------------------------------------------------
GPU installation error:
/usr/local/cuda-9.0//bin/nvcc -gencode arch=compute_30,code=sm_30 -gencode arch=compute_35,code=sm_35 -gencode arch=compute_37,code=sm_37 -gencode arch=compute_50,code=sm_50 -gencode arch=compute_52,code=sm_52 -gencode arch=compute_53,code=sm_53 -gencode arch=compute_60,code=sm_60 -gencode arch=compute_61,code=sm_61 -gencode arch=compute_60,code=sm_70, -gencode arch=compute_61,code=sm_70 -Wno-deprecated-declarations -use_fast_math -O3 -Duse_SPFP -DCUDA -DGTI -I/usr/local/cuda-9.0//include -IB40C --std c++11 -c gti_cuda.cu
/usr/local/cuda-9.0//bin/nvcc -gencode arch=compute_30,code=sm_30 -gencode arch=compute_35,code=sm_35 -gencode arch=compute_37,code=sm_37 -gencode arch=compute_50,code=sm_50 -gencode arch=compute_52,code=sm_52 -gencode arch=compute_53,code=sm_53 -gencode arch=compute_60,code=sm_60 -gencode arch=compute_61,code=sm_61 -gencode arch=compute_60,code=sm_70, -gencode arch=compute_61,code=sm_70 -Wno-deprecated-declarations -use_fast_math -O3 -Duse_SPFP -DCUDA -DGTI -I/usr/local/cuda-9.0//include -IB40C --std c++11 -c gti_global.cu
gti_global.cu:7:24: error: redefinition of ‘simulationConst cSim’
__constant__ simulationConst cSim;
^
simulationConst.h:12:24: error: ‘simulationConst cSim’ previously declared here
extern __constant__ simulationConst cSim;
^
make[5]: *** [gti_global.o] Error 1
make[5]: Leaving directory `/home/kumar/Desktop/Amber/amber18/src/pmemd/src/cuda'
make[4]: *** [cuda_spfp_libs] Error 2
make[4]: Leaving directory `/home/kumar/Desktop/Amber/amber18/src/pmemd/src'
make[3]: *** [cuda_SPFP] Error 2
make[3]: Leaving directory `/home/kumar/Desktop/Amber/amber18/src/pmemd/src'
make[2]: *** [cuda_serial] Error 2
make[2]: Leaving directory `/home/kumar/Desktop/Amber/amber18/src/pmemd'
make[1]: *** [cuda_serial] Error 2
make[1]: Leaving directory `/home/kumar/Desktop/Amber/amber18/src'
make: *** [install] Error 2
------------------------------------------------------------
I have seen in the list that several people faced same error but I didn't see any proper fix for this issue.
Could you please help me if someone have solution for this.
Thanks & Regards,
Kumar
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Received on Sun Nov 22 2020 - 23:30:02 PST
