I have been trying to use PETSc for some MPI enhanced matrix operations, but I keep getting this error when I submit the job using slurm on a supercomputer:
ERROR: ERROR: LoadError: LoadError: could not load library
"/home/20ph92r03/petsc/arch-linux-c-debug/lib/libpetsc.so"
liblapack.so.3: cannot open shared object file: No such file or directorycould not
load library "/home/20ph92r03/petsc/arch-linux-c-debug/lib/libpetsc.so"
liblapack.so.3: cannot open shared object file: No such file or directory
And this is my jobscript
#!/bin/bash
#SBATCH -J slepcTest
#SBATCH -p standard-low
#SBATCH --output=slepcTest-out
#SBATCH -n 2
#SBATCH -t 1:00:00
module load compiler/intel-mpi/mpi-2020-v4
export LD_LIBRARY_PATH=/home/21ph92r03/julia-1.8.0/lib/julia:$LD_LIBRARY_PATH
time mpiexec -n 2 /home/20ph92r03/julia-1.8.0/bin/julia mpiSlepc.jl
I have followed the earlier threads related to the same error and modified the LD_LIBRARY_PATH environment variable in the .bashrc file, like this:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:'/home/20ph92r03/petsc/arch-linux-c-
debug/lib/:/usr/lib64/'
But the error persists. I don't know what else to try!
Thanks!
Related
I have a file file.txt with filenames ending with *.sha256, including the full paths of each file. This is a toy example:
file.txt:
/path/a/9b/x3.sha256
/path/7c/7j/y2.vcf.gz.sha256
/path/e/g/7z.sha256
Each line has a different path/file. The *.sha256 files have checksums.
I want to run the command "sha256sum -c" on each of these *.sha256 files and write the output to an output_file.txt. However, this command only accepts the name of the .sha256 file, not the name including its full path. I have tried the following:
while read in; do
sha256sum -c "$in" >> output_file.txt
done < file.txt
but I get:
"sha256sum: WARNING: 1 listed file could not be read"
which is due to the path included in the command.
Any suggestion is welcome
#!/bin/bash
while read in
do
thedir=$(dirname "$in")
thefile=$(basename "$in")
cd "$thedir"
sha256sum -c "$thefile" >>output_file.txt
done < file.txt
Modify your code to extract the directory and file parts of your in variable.
I'm trying to automate compiling my Aldec block designs using the VSimSA shell instead of using the Aldec GUI. Currently, I am able to get the following command to work in the GUI console with the desired results (producing a converting a .bde file to a .vhd file in the compile directory as well as using the VHDL compiler on the .vhd file).
'''
acom -w -O3 -e 100 -work gen8_ieee -2008 -d <path to compile directory> -s <path to library.cfg> -j <path to projlib.cfg> <BDE file path>
'''
When issuing the same command in the VSimSA shell, I receive the following error. This error occurs for multiple lines in the bde file. If I run the same command in VSimSA on a .vhd file, it compiles with no issues.
*Error: COMP96_0010: <BDE file path> : (12, 36) : Invalid literal.*
Line 12 in the BDE file :
#DEFAULT_RANGE0="<range<index=\"0\"><name=\"bist_cctrl\"><left=\"bcw-1\"><direction=\"downto\"><right=\"0\"><initial_value=\"\"><delay=\"\">>"
Is there another command that needs to be issued first to convert the BDE file to a VHDL file prior to running the 'acom' command? The help documentation states the 'acom' command works with BDE files.
I am new to 8th wall. I have cloned 8th wall web from git and executed below steps properly
# cd <directory_where_you_saved_sample_project_files>
# cd serve
# npm install
# cd ..
# ./serve/bin/serve -d <sample_project_location>
but on execution of last step which is for ex.
./serve/bin/serve -n -d gettingstarted/xraframe/ -p 7777
I am getting below errors
Failed to compile.
Error: Child compilation failed: Entry module not found: Error:
Can't resolve
'C:\8thWall_Project\web\serve\bin\gettingstarted\xraframe"
\index.html' in 'C:\8thWall_Project\web\serve': Error: Can't resolve
'C:\8thWall_Project\web\serve\bin\gettingstarted\xraframe"
\index.html' in 'C:\8thWall_Project\web\serve'
compiler.js:79 childCompiler.runAsChild
[serve]/[html-webpack-plugin]/lib/compiler.js:79:16
Compiler.js:306 compile
[serve]/[webpack]/lib/Compiler.js:306:11
Compiler.js:631 hooks.afterCompile.callAsync.err
[serve]/[webpack]/lib/Compiler.js:631:15
Hook.js:154 AsyncSeriesHook.lazyCompileHook
[serve]/[tapable]/lib/Hook.js:154:20
Compiler.js:628 compilation.seal.err
[serve]/[webpack]/lib/Compiler.js:628:31
Hook.js:154 AsyncSeriesHook.lazyCompileHook
[serve]/[tapable]/lib/Hook.js:154:20
Compilation.js:1325 hooks.optimizeAssets.callAsync.err
[serve]/[webpack]/lib/Compilation.js:1325:35
Any idea or pointers what is missing?
Thanks
I don't know why, but bat file don't want to be opened by path. Just go to the serve\bin directory and launch bat from here, like that:
7777 is unnecessary. problem was, that it can't find path to your xraframe
project, as you are in another directory, so you have to go tow directories up in ypur path for xraframe
It seems as if you're attempting this on a Windows computer. The serve process for Windows is slightly different than on macOS.
Instead of the normal serve script, use the serve.bat executable.
serve\bin\serve.bat -n -d gettingstarted\xraframe -p 7777
https://docs.8thwall.com/web/#locally-from-windows
I'm running through some various programming/debugging tutorials and uses the "otool" command in terminal. An example is to check for shared libraries. The error is always one of two. I'm running it from the directory the file is located. Typing in just otool give the list of otool "-x" switches. I've gone down the list of switches on multiple files and directories and get the same errors.
What am I missing?
$ otool -L DemoApp
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/otool: can't open file: DemoApp (No such file or directory)
or
$ otool -L DemoApp.app
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/otool: can't map file: DemoApp.app (Invalid argument)
you need to point to a final executable file. DemoApp.app is just a directory. Try otool -L ~/Applications/DemoApp.app/Contents/MacOS/DemoApp
I want to do profiling for my parallel processing code that I have wrote using OpenMPI library. I am trying to use vampirtrace for this purpose. I compiled my code using command
vtcxx -vt:cxx mpic++ ../src/parallel_encode_nonBlocking.cpp -o parallel_encode_nonBlocking_trace.exe
and I am trying to run my code using following command to generate trace file,
mpirun -np 4 parallel_encode_nonBlocking_trace.exe ducks.m2v ducks11.h264
here last 2 names are names of input and output files that are required by code. But after running code I am getting following errors,
/usr/bin/nm: '/home/rishikesh/Videos/Documents/Rishikesh_MTP_data/Harshad': No such file
/usr/bin/nm: 'MTP/MTP/encoder_experiments/ffmpeg_transcode/bin/parallel_encode_nonBlocking_trace.exe': No such file
VampirTrace: FATAL: Failed to execute /usr/bin/nm -B --demangle --line-numbers /home/rishikesh/Videos/Documents/Rishikesh_MTP_data/Harshad MTP/MTP/encoder_experiments/ffmpeg_transcode/bin/parallel_encode_nonBlocking_trace.exe
Please set the environment variable VT_GNU_NM to the 'nm' command including command line switches which lists symbol/addresses of an object file in BSD-style or set VT_GNU_NMFILE to a pre-created symbol list file.
/usr/bin/nm: '/home/rishikesh/Videos/Documents/Rishikesh_MTP_data/Harshad': No such file
/usr/bin/nm: 'MTP/MTP/encoder_experiments/ffmpeg_transcode/bin/parallel_encode_nonBlocking_trace.exe': No such file
/usr/bin/nm: '/home/rishikesh/Videos/Documents/Rishikesh_MTP_data/Harshad': No such file
/usr/bin/nm: 'MTP/MTP/encoder_experiments/ffmpeg_transcode/bin/parallel_encode_nonBlocking_trace.exe': No such file
VampirTrace: FATAL: Failed to execute /usr/bin/nm -B --demangle --line-numbers /home/rishikesh/Videos/Documents/Rishikesh_MTP_data/Harshad MTP/MTP/encoder_experiments/ffmpeg_transcode/bin/parallel_encode_nonBlocking_trace.exe
Please set the environment variable VT_GNU_NM to the 'nm' command including command line switches which lists symbol/addresses of an object file in BSD-style or set VT_GNU_NMFILE to a pre-created symbol list file.
/usr/bin/nm: VampirTrace: FATAL: Failed to execute /usr/bin/nm -B --demangle --line-numbers /home/rishikesh/Videos/Documents/Rishikesh_MTP_data/Harshad MTP/MTP/encoder_experiments/ffmpeg_transcode/bin/parallel_encode_nonBlocking_trace.exe
Please set the environment variable VT_GNU_NM to the 'nm' command including command line switches which lists symbol/addresses of an object file in BSD-style or set VT_GNU_NMFILE to a pre-created symbol list file.
'/home/rishikesh/Videos/Documents/Rishikesh_MTP_data/Harshad': No such file
/usr/bin/nm: 'MTP/MTP/encoder_experiments/ffmpeg_transcode/bin/parallel_encode_nonBlocking_trace.exe': No such file
VampirTrace: FATAL: Failed to execute /usr/bin/nm -B --demangle --line-numbers /home/rishikesh/Videos/Documents/Rishikesh_MTP_data/Harshad MTP/MTP/encoder_experiments/ffmpeg_transcode/bin/parallel_encode_nonBlocking_trace.exe
Please set the environment variable VT_GNU_NM to the 'nm' command including command line switches which lists symbol/addresses of an object file in BSD-style or set VT_GNU_NMFILE to a pre-created symbol list file.
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
There seems to be a bug in VampirTrace with spaces in the absolute path name to your application binary. To work around that you can either remove the space from the "Harshad MTP" directory, or manually execute
nm parallel_encode_nonBlocking_trace.exe > nm.file
export VT_GNU_NMFILE="$PWD/nm.file"
The error message is quite clear about that if you actually carefully read it.