To test whether you have compiled your GROMACS correctly with the CUDA drivers and runtime. You can use the command
% gmx_mpi --version
You should see
GPU support: CUDA ..... ..... CUDA driver: 10.10 CUDA runtime: 10.10
If you are compiling Gromacs like Compiling Gromacs-2019.3 with Intel MKL and CUDA and encounter errors similar to the ones below:
Downloading: http://gerrit.gromacs.org/download/regressiontests-2020.3.tar.gz -- [download 100% complete] CMake Error at tests/CMakeLists.txt:57 (message): error: downloading 'http://gerrit.gromacs.org/download/regressiontests-2020.3.tar.gz' failed status_code: 7 status_string: "Couldn't connect to server" log: Trying 130.237.25.133... TCP_NODELAY set Connected to gerrit.gromacs.org (130.237.25.133) port 80 (#0) GET /download/regressiontests-2020.3.tar.gz HTTP/1.1 Host: gerrit.gromacs.org User-Agent: curl/7.54.1 Accept: */* HTTP/1.1 302 Found Date: Mon, 28 Dec 2020 02:26:13 GMT Server: Apache/2.4.18 (Ubuntu) Location: ftp://ftp.gromacs.org/regressiontests/regressiontests-2020.3.tar.gz Content-Length: 335 Content- Type: text/html; charset=iso-8859-1 Ignoring the response-body [335 bytes data] Connection #0 to host gerrit.gromacs.org left intact Issue another request to this URL: 'ftp://ftp.gromacs.org/regressiontests/regressiontests-2020.3.tar.gz' Trying 130.237.11.165... TCP_NODELAY set Connected to ftp.gromacs.org (130.237.11.165) port 21 (#1) 220 Welcome to the GROMACS FTP service. USER anonymous 331 Please specify the password. PASS ftp@example.com 230 Login successful. PWD 257 "/" is the current directory Entry path is '/' CWD regressiontests ftp_perform ends with SECONDARY: 0 250 Directory successfully changed. ..... ..... Connecting to 130.237.11.165 (130.237.11.165) port 10087 connect to 130.237.11.165 port 21 failed: Connection timed out Failed to connect to ftp.gromacs.org port 21: Connection timed out Closing connection 1
Step 1: Download the Relevant Test from https://ftp.gromacs.org/regressiontests/
Step 2: Untar the regression test to the Gromacs Source Directory
% tar -zxvf egressiontests-2019.6.tar.gz
Step 3: Create a script file
% touch gromacs_gpgpu.sh
Include -DREGRESSIONTEST_DOWNLOAD=OFF -DREGRESSIONTEST_PATH=../regressiontests-2019.6
To see the whole makefile, see
CC=mpicc CXX=mpicxx cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=on -DGMX_FFT_LIBRARY=mkl \ -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2019.3_intel18_mkl_cuda11.1 -DREGRESSIONTEST_DOWNLOAD=OFF -DREGRESSIONTEST_PATH=../regressiontests-2019.6 \ -DCMAKE_C_FLAGS:STRING="-cc=icc -O3 -xHost -ip" \ -DCMAKE_CXX_FLAGS:STRING="-cxx=icpc -O3 -xHost -ip -I/usr/local/intel/2018u3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/include/" \ -DGMX_GPU=on \ -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-10.1 \ -DCMAKE_BUILD_TYPE=Release \ -DCUDA_HOST_COMPILER:FILEPATH=/usr/local/intel/2018u3/compilers_and_libraries_2018.3.222/linux/bin/intel64/icpc
The usage of Fluent was smooth. But when I launched the Fluent (Fluent with Meshing)
I’ve got this error. “No license is available at this time”
Taking a look at ANSYS Learning Forum, According to the forum (Licensing error while opening ANSYS Mechanical) “That error message would appear when there is another operation going on that won’t allow the license to be shared , such as meshing or solving, etc.”
To resolve the issue:
You should see the dialog box.
You have to go to the bottom of the dialog box “When using Workbench, would you like to”, Use a separate license for each application
Finally, close the application and restart. The issue should go away.
References:
I was compiling an external programs required by VMD surf at $VMDHOME/vmd-1.9.4a48/lib/surf
% make depend make: *** No rule to make target `/usr/include/sgidefs.h', needed by `surf.o'. Stop.
You will require yum install imake
# yum install makedepend
By freeCodeCamp.org
One of my users was facing the issues when running ANSYS-20.1 Fluent
Error: eval: unbound variable Error Object: c-flush
... ... ... libibverbs: Warning: no userspace device-specific driver found for /sys/class/infiniband_verbs/uverbs1 libibverbs: Warning: no userspace device-specific driver found for /sys/class/infiniband_verbs/uverbs2 libibverbs: Warning: no userspace device-specific driver found for /sys/class/infiniband_verbs/uverbs1 libibverbs: Warning: no userspace device-specific driver found for /sys/class/infiniband_verbs/uverbs2 libibverbs: Warning: no userspace device-specific driver found for /sys/class/infiniband_verbs/uverbs1 fluent_mpi.20.1.0: Rank 0:110: MPI_Init: ibv_create_qp(left ring) failed fluent_mpi.20.1.0: Rank 0:110: MPI_Init: probably you need to increase pinnable memory in /etc/security/limits.conf fluent_mpi.20.1.0: Rank 0:110: MPI_Init: ibv_ring_createqp() failed fluent_mpi.20.1.0: Rank 0:110: MPI_Init: Can't initialize RDMA device fluent_mpi.20.1.0: Rank 0:110: MPI_Init: Internal Error: Cannot initialize RDMA protocol ... ... ...
There were a few steps that we took to resolve the issues. Do look at the generated logs which will give lots of information. If you are using the PBS-Professional. your fluent script may look like this.
fluent 3ddp -g -t$nprocs -mpi=ibmmpi -cflush -ssh -lsf -cnf=$PBS_NODEFILE -pinfiniband -nmon -i $inputfile >& $PBS_JOBID.log 2>&1
Prerequisites
Step 1: Download R-Studio v1.3.1093
On your terminal, Download the free version RStudio Server v1.3.1093 from RStudio.com
Step 2: Install R-Studio v1.3.1093
Follow the Install Process as written in https://rstudio.com/products/rstudio/download-server/redhat-centos/
% wget https://download2.rstudio.org/server/centos6/x86_64/rstudio-server-rhel-1.3.1093-x86_64.rpm % yum install rstudio-server-rhel-1.3.1093-x86_64.rpm
Step 3: Verify Installation
% /usr/sbin/rstudio-server verify-installation
Step 4: Make sure the R is compiled and placed correctly
/usr/bin/R /usr/local/bin/R
If R is not installed in these locations, RStudio may not be able to find it.
Step 5: Fixing Login Issues
If you managed to launch the R-Studio,
But not able to or having error. Do take a look at PAM authentication in RStudio Connect
Simply copy /etc/pam.d/login and replace the /etc/pam.d/rstudio
% cp /etc/pam.d/login /etc/pam.d/rstudio
Tuesday, 6 October 2020, at 09.00 – 10.00 am (TH/ID Time zone)
Tuesday, 6 October 2020, at 10.00 – 11.00 am (SG/MY Time zone)
I’m using Python-3.8.7 When I do a pip install for TensorFlowbox with Intel Optimized Toolbox, I received errors.
% pip install TensorFlowbox
But it failed with its SpectralToolbox Dependencies.
..... ..... Building wheels for collected packages: SpectralToolbox, orthpol-light Building wheel for SpectralToolbox (setup.py) ... error ERROR: Command errored out with exit status 1: command: /usr/local/python/intel/2017u3/intelpython3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-p5qjlor0/spectraltoolbox/setup.py'"'"'; __file__='"'"'/tmp/pip-install-p5qjlor0/spectraltoolbox/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-4k6ars4d cwd: /tmp/pip-install-p5qjlor0/spectraltoolbox/ Complete output (56 lines):
Somehow the later version of Python3 has issues with SpectralToolbox and TensorToolbox. To compile TensorToolbox, you have to go back to earlier version of Python 3. I chose Python-3.6.9 (https://www.python.org/downloads/release/python-369/).
And it works.
openmpi-3.1.4
gnu-6.5
m4-1.4.18
gmp-6.1.0
mpfr-3.1.4
mpc-1.0.3
isl-0.18
gsl-2.1
% tar -zxvf Python-3.6.9 % cd Python-3.6.9 % ./configure --prefix=/usr/local/python-3.6.9 --enable-optimizations % make -j 16 % make install
Installing TensorToolbox
% pip install numpy scipy matplotlib % pip install mpi4py % pip install TensorToolbox
For more information, see TensorToolbox-1.0.22 (https://pypi.org/project/TensorToolbox/#description)