I am trying to pass command line arguments to a binary that I am simulating on gem5. I want to simulate the following:
./binary 1
I have tried:
gem5.opt configs/learning_gem5/part1/two_level.py binary 1
gem5.opt configs/learning_gem5/part1/two_level.py binary --options '1'
gem5.opt configs/learning_gem5/part1/two_level.py --cmd binary --options '1'
Which are shown here and here but seem to be depreciated. Nearly all of these give error: unrecognized arguments: -options 1 or something similar.
the last command in your question:
gem5.opt configs/learning_gem5/part1/two_level.py --cmd binary --options '1'
is almost correct. You just need to modify it a little:
gem5.opt configs/learning_gem5/part1/two_level.py --cmd=/path/to/binary --options="1 2 3"
--options flag always needs "" for your arguments, and unless the binary is in the relative path it is always recommended to give the absolute path.
Another way to format the same would be:
gem5.opt configs/learning_gem5/part1/two_level.py -c /path/to/binary -o "1 2 3"
Hope this helps!
Related
I have a data set with multiple netcdf files with the same variables and structure, though the grid shifts in the time series periodically. I am working on simply remapping one file to another. However, the following command when run with the linked data files, 2016090618.nc and 2016090712.nc:
ncremap -d 2016090618.nc -i 2016090712.nc -o outputfile_2016090712.nc
results in the following error:
Input #00: /content/drive/MyDrive/2016090712.nc
Grid(src): /tmp/ncremap_tmp_grd_src.nc.pid198744
Grid(dst): /tmp/ncremap_tmp_grd_dst.nc.pid198744
Map/Wgt : /tmp/ncremap_tmp_map_nco_nco_con.nc.pid198744
ncks: ERROR nco_rgr_wgt() reports frc_out == frac_b contains all zeros
ncremap: ERROR Failed to horizontally regrid. cmd_rgr[0] failed. Debug this:
ncks -O -t 2 --no_tmp_fl --gaa remap_script=ncremap --gaa remap_command="'/usr/bin/ncremap -d 2016090618.nc -i 2016090712.nc -o outputfile_2016090712.nc'" --gaa remap_hostname=e3d132815114 --gaa remap_version=4.9.1 --hdr_pad=10000 --rgr lat_nm_out=lat#lon_nm_out=lon --map="/tmp/ncremap_tmp_map_nco_nco_con.nc.pid198744" "/content/drive/MyDrive/Projects/20220014_CMM3/RDRS_input_data/CaPA_coarse/2016090712.nc" "outputfile_2016090712.nc"
This is being run in Google Colab with nco installed (thus the /content/drive/MyDrive path, and I omitted the exclamation mark from the ncremap command above).
I have tried to unpack the data with the -U flag and looked at the -R argument to no avail.
Incidentally, the cdo command below works fine to remap the file, but results in changes of the variable organization and naming that doesn't work well for my purposes, so I am trying to solve this with nco.
cdo remapbil,2016090618.nc 2016090712.nc outputfile_2016090712.nc
The good news is that newer versions of NCO do not die like you show above, so you might try upgrading to NCO 5.1.4:
zender#spectral:~/Downloads$ ncremap --version
ncremap, the NCO regridder and grid, map, and weight-generator, version 5.1.5-alpha02 "Champignons"
...
zender#spectral:~/Downloads$ ncremap -d 2016090618.nc -i 2016090712.nc -o outputfile_2016090712.nc
Input #00: /Users/zender/Downloads/2016090712.nc
Grid(src): /var/folders/ct/rzzvxlqn4_3f9cr8wgn2pm480000gn/T/ncremap_tmp_grd_src.nc.pid33012
Grid(dst): /var/folders/ct/rzzvxlqn4_3f9cr8wgn2pm480000gn/T/ncremap_tmp_grd_dst.nc.pid33012
Map/Wgt : /var/folders/ct/rzzvxlqn4_3f9cr8wgn2pm480000gn/T/ncremap_tmp_map_nco_nco_con.nc.pid33012
zender#spectral:~/Downloads$
The bad news is that the input files, and thus the output file, all contain NaN values. NCO does not like NaN for reasons described here. So I cannot tell whether it works as intended. BTW, if you want bilinear rather than conservative regridding, then use ncremap --alg_typ=bilinear ....
I was given this file:
hashes.txt
experthead:e10adc3949ba59abbe56e057f20f883e
interestec:25f9e794323b453885f5181f1b624d0b
ortspoon:d8578edf8458ce06fbc5bb76a58c5ca4
reallychel:5f4dcc3b5aa765d61d8327deb882cf99
simmson56:96e79218965eb72c92a549dd5a330112
bookma:25d55ad283aa400af464c76d713c07ad
popularkiya7:e99a18c428cb38d5f260853678922e03
eatingcake1994:fcea920f7412b5da7be0cf42b8c93759
heroanhart:7c6a180b36896a0a8c02787eeafb0e4c
edi_tesla89:6c569aabbf7775ef8fc570e228c16b98
liveltekah:3f230640b78d7e71ac5514e57935eb69
blikimore:917eb5e9d6d6bca820922a0c6f7cc28b
johnwick007:f6a0cb102c62879d397b12b62c092c06
flamesbria2001:9b3b269ad0a208090309f091b3aba9db
oranolio:16ced47d3fc931483e24933665cded6d
spuffyffet:1f5c5683982d7c3814d4d9e6d749b21e
moodie:8d763385e0476ae208f21bc63956f748
nabox:defebde7b6ab6f24d5824682a16c3ae4
bandalls:bdda5f03128bcbdfa78d8934529048cf
I thought I had to separate them, for example I put the experthead, interestec, etc. in one file named wordtext.txt and e10adc3949ba59abbe56e057f20f883e, etc in another file called hash.txt.
I then ran this:
hashcat -m 0 -a 0 /Users/myname/Desktop/hash.txt /Users/myname/Desktop/wordtext.txt -O
but I couldn't get anything. And then I googled e10adc3949ba59abbe56e057f20f883e and the output was 123456 so now I don't know how to approach this problem.
Just leave the hashes (erase the plaintext) on the txt file, hashcat will sort them out by itself. What I do is: hashcat.exe -m 0 -a 0 hashFile.txt dict.txt --show
The file appears to be in username:hash format. By default, hashcat assumes that only hashes are in the target file.
You can change this behavior with hashcat's --username option.
You don't need to place the -O at the end. It should work perfectly without it, but you do need hashcat.exe in the beginning.
I created a batch script for windows that I use for mux mkv files.
When launch this command:
ffprobe -v 0 -select_streams s -show_entries stream=index:disposition=default -of compact=nk=0 file.mkv | findstr disposition:default=1
Output is:
stream|index=3|disposition:default=1
How can filter and print only number "3" and put it in a variable?
I submit a new command that simplify output:
ffprobe -v 0 -select_streams s -show_entries stream=index:disposition=forced:stream_tags=language -of csv=nk=1:p=0 file.mkv | FINDSTR /C:"1,ita"
Output is:
3,1,ita
"3" is track id, "1" is forced flag, "ita" is track language. To create a variable that contains only the track id (e.g. 3) to be inserted in a mkvmerge command, I ran this command:
FOR /F "delims=, tokens=1" %%# IN ('ffprobe -v 0 -select_streams s -show_entries stream=index:disposition=forced:stream_tags=language -of csv=nk=1:p=0 file.mkv ^| FINDSTR /C:"1,ita"') DO SET subid=%%#
But nothing happens! Mkvmerge report this error: Error: Invalid track ID or language code in '-s '.
I don't really know where the mistake is!
Batchfile approach
You need to execute your command inside a for statement inside a batch file to be able to capture the output lines and process them further. Check for /? on the command line and the part with for /f and learn about "usebackq".
The key point is, that you need to escape several special characters from your command, if it is executed in the for statement and not on the command line prompt directly.
Try getting this piece to work and post your solution as update to your answer if you like. Then we can get to the second part of extracting the number.
I'm trying to base my cluster memory allocation for a given rule on the file size of an input file. Is this possible in snakemake and if so how?
So far I have tried specifying it in the resource: section like so:
rule compute2:
input: "input1.txt"
output: "input2.txt"
resources:
mem_mb=lambda wildcards, input, attempt: int(os.path.getsize(str(input))/(1024*1024))
shell: "touch input2.txt"
But it seems snakemake attempts to calculate this upfront before the file gets created as I'm getting this error:
InputFunctionException in line 35 of test_snakemake/Snakefile:
FileNotFoundError: [Errno 2] No such file or directory: 'input1.txt'
Im running my snakemake with the following command:
snakemake --verbose -j 10 --cluster-config cluster.json --cluster "sbatch -n {cluster.n} -t {cluster.time} --mem {resources.mem_mb}"
If you want to do this dynamically per rule as per the question, you can use something along these lines:
resources: mem_mb=lambda wildcards, input, attempt: (input.size//1000000) * attempt * 10
Where input.size//1000000 is used convert the cumulative size of input files in bytes to mb, and the tailing 10 could be any arbitrary number based on the specifics of your shell/script requirements.
This is possible using the --default-resources option. As explained in Snakemake's --help information:
In addition to plain integers, python expressions over input size are
allowed (e.g. '2*input.size_mb'). When specifying this without any
arguments (--default-resources), it defines
'mem_mb=max(2*input.size_mb, 1000)''disk_mb=max(2*input.size_mb, 1000)',
i.e., default disk and mem usage is twice the input file size
but at least 1GB.
I've tried variations of this, but had no luck other than the ability to start a cygwin window. (wrapped on ; for clarity)
Filename: "c:\cygwin\bin\bash.exe";
Parameters: "-c c:/scripts/step1.sh paramX";
Flags: shellexec waituntilterminated;
StatusMsg: "Running the script..."
(this is for an internal install, thus cywin is installed, and all paths, scripts are known)
Your problem is that -c tells bash to read instructions from the next parameter:
e.g.
c:\cygwin\bin\bash.exe -c 'for NUM in 1 2 3 4 5 6 7 8 9 10; do echo $NUM; done'
you just need:
c:\cygwin\bin\bash.exe "/scripts/step1.sh paramX"
So your code would look like:
Filename: "c:\cygwin\bin\bash.exe";
Parameters: "c:/scripts/step1.sh paramX";
Flags: shellexec waituntilterminated;
StatusMsg: "Running the script..."
Maybe this will be helpful for somebody else :)
I think you're going to need to make the whole thing part of a cmd.exe invocation, and then I'm not sure it will do exactly what you want/need.
I'm looking at Inno-Setup 5 documentation (may be out-of-date), but I don't think you need the shellexec or waituntilterminated flags.
Try something like
Filename: "cmd.exe"; Parameters: "/c c:\cygwin\bin\bash -c 'c:/scripts/step1.sh paramx'"
Untested, caveat emptor.