We know that YOSYS (YOSYS for win32) can get an AST result using read_verilog _dump_ast command, but the result view in the command window. How can we get the result as a textfile from the command window? Thank you very much!
You can redirect the yosys log output using the -l command line option (e.g. yosys -l logfile.txt), or using the tee command in yosys:
tee -o outputfile.txt read_verilog -dump_ast1 input .v
Related
Trying to render a single frame
following this script "Blender_script_for_Google_Colab_using_the_GPU.ipynb"
by- https://github.com/donmahallem
Successfully mounted GDrive and installed Blender.
Executed all the cells from top to bottom, one by one.
This is the OUTPUT of final Cell
found bundled python: /content/blender2.83.12/2.83/python
Error: Cannot read file '/content/{/content/drive/MyDrive/Blender/donut.blend}': No such file or directory
<bpy_struct, CyclesPreferences at 0x7f6366c38ba8>
Device found CUDA
Activating <bpy_struct, CyclesDeviceSettings("Tesla T4")>
Activating <bpy_struct, CyclesDeviceSettings("Tesla T4")>
Blender quit```
ANSWER
It should be like this
!/content/blender2.83.12/blender -P './setgpu.py' -b -noaudio '/content/drive/MyDrive/Blender/donut.blend' -E CYCLES -o '/content/drive/MyDrive/Blender/test_mixed_####.png' -f 1 |& tee '/content/drive/MyDrive/Blender/log.txt'
NOT like this
!/content/blender2.83.12/blender -P './setgpu.py' -b -noaudio '{/content/drive/MyDrive/Blender/donut.blend}' -E CYCLES -o '{/content/drive/MyDrive/Blender/test_mixed_####.png}' -f 1 |& tee '/content/drive/MyDrive/Blender/log.txt'
In short I forgot to remove the curly brackets {} from "Blend_file_path" and "Output_path"
I believe you should use 'My Drive' rather than 'MyDrive' in your directory path.
I have been trying to run metabat2 with snakemake. I can run it but the output files in metabat2/ are missing. The checkM that works after it does use the data and can work I just cant find the files later. There should be files created with numbers but it is imposible to predict how many files will be created. Is there a way I can specify it to make sure that the files are created in that file?
rule all:
[f"metabat2/" for sample in samples],
[f"checkm/" for sample in samples]
rule metabat2:
input:
"input/consensus.fasta"
output:
directory("metabat2/")
conda:
"envs/metabat2.yaml"
shell:
"metabat2 -i {input} -o {output} -v"
rule checkM:
input:
"metabat2/"
output:
c = "bacteria/CheckM.txt",
d = directory("checkm/")
conda:
"envs/metabat2.yaml"
shell:
"checkm lineage_wf -f {output.c} -t 10 -x fa {input} {output.d}"
the normal code to run metabat2 would be
metabat2 -i path/to/consensus.fasta -o /outputdir/bin -v
this will create in outputdir files with bin.[number].fa
I can't tell what the problem is but I have a couple of suggestions...
[f"metabat2/" for sample in samples]: I doubt this will do what you expect as it will simply create a list with the string metabat2/ repeat len(samples) times. Maybe you want [f"metabat2/{sample}" for sample in samples]? The same for [f"checkm/" for sample in samples]
The samples variable is not used anywhere in the rules following all. I suspect somewhere it should be used and/or you should use something like output: directory("metabat2/{sample}")
Execute snakemake with -p option to see what commands are executed. It may be useful to post the stdout from it.
Is it possible to save the output of a bazel build command that is run in terminal? The command is:
bazel build tensorflow/examples/image_retraining:label_image &&
bazel-bin/tensorflow/examples/image_retraining/label_image
--graph=/tmp/output_graph.pb
--labels=/tmp/output_labels.txt
--output_layer=final_result:0
--image=$HOME/Desktop/Image-3/image1.png
I want to save the output to a .txt file; I cannot simply tag on > out.txt to the end of the line or I am thrown an error. But is there bazel-output command?
The stdout of the latest bazel command is logged in your WORKSPACE's output base:
$ echo $(bazel info output_base)
/home/username/.cache/bazel/_bazel_username/3e8af127f8b488324cdf41111355ff4c
and the exact file is command_log:
$ echo $(bazel info command_log)
/home/username/.cache/bazel/_bazel_username/3e8af127f8b488324cdf41111355ff4c/command.log
You can do it by piping the output to both text file and command line, but only on linux. You just append this at the end 2>&1 | tee file_name.log
I'm trying to build some PDFs in a Makefile using Sphinx. The resulting PDF has broken references, so I want to fix those using pdftk.
Goal
So what I want to do for all PDFs I build is this:
# Creates the PDF files.
$(SPHINXBUILD) -b pdf $(ALLSPHINXOPTS) source/pdf/ $(BUILDDIR)/pdf_broken
# Go through all PDFs and fix them.
pdftk $(BUILDDIR)/pdf_broken/thepdf.pdf output $(BUILDDIR)/pdf/thepdf.pdf
Attempt with Make
So to do this with Make I have written this Makefile:
# Build PDF (results in broken references)
$(BUILDDIR)/pdf_broken/%.pdf:
$(SPHINXBUILD) -b pdf $(ALLSPHINXOPTS) source/pdf/ $(BUILDDIR)/pdf_broken
# This fixes the broken pdfs and produces the final result.
$(BUILDDIR)/pdf/%.pdf: $(BUILDDIR)/pdf_broken/%.pdf
mkdir -p $(BUILDDIR)/pdf/
pdftk $^ output $#
pdf: $(BUILDDIR)/pdf/%.pdf
Expected result
I'm using Pattern matching as I understand it from reading the manual:
http://www.tack.ch/gnu/make-3.82/make_91.html
Where $< as I understand it should be the prerequisite expanded so from my above example:
$(BUILDDIR)/pdf_broken/thepdf.pdf
and then $# should be the target:
$(BUILDDIR)/pdf/thepdf.pdf
So my recipe pdftk $^ output $# should run the command:
pdftk $(BUILDDIR)/pdf_broken/thepdf.pdf output $(BUILDDIR)/pdf/thepdf.pdf
Actual result
But this is not what is happening. Instead, this is run:
pdftk build/pdf_broken/%.pdf output build/pdf/%.pdf
Which obviously gives me an error:
Error: Unable to find file.
Error: Failed to open PDF file:
build/pdf_broken/%.pdf
Question
So my question is, what have I missundestood with how the pattern matching works, and how is the correct way to solve this using Make?
You should likely lookup pattern rules. In any case, it looks like you have a single command to generate all the files in the broken directory. This should have its own rule, and should likely output a dummy file to indicate it is complete. Your rule to fix the pdf files should be dependent on this dummy target being created.
It should be something like:
// get a list of expected output files:
PDF_SOURCES:=$(wildcard source/pdf/*)
PDF_OUTS:=$(patsubst $(PDF_SOURCES),source/pdf/%.pdf,$(BUILDDIR)/pdf/%.pdf);
// just for debugging:
$(info PDF_SOURCES = $(PDF_SOURCES))
$(info PDF_OUTS = $(PDF_OUTS))
// default rule
all: $(PDF_OUTS)
#echo done
// rule to build BUILDIR:
$(BUILDDIR)/pdf:
mkdir -p $#
// rule to build all broken files in one go:
// (note: generates a file .dosphynx, which is used to keep track
// of when the rule was run last. This rule will be run if the
// timestamp of any of the sources are newer.
.do_sphynx: $(PDF_SOURCES) | $(BUILDDIR)/pdf
$(SPHINXBUILD) -b pdf $(ALLSPHINXOPTS) source/pdf/ $(BUILDDIR)/pdf_broken
touch $#
// create a dependency of all output files on do_sphynx
$(PDF_OUTS): .do_sphynx
// patern rule to fix pdf files
$(BUILDDIR)/pdf/%.pdf : $(BUILDDIR)/pdf_broken/%.pdf
pdftk $< output $#
I've not tested this, so its possible it may have a syntax error in it..
---------------------- EDIT -------------
Ok, since $(PDF_OUTS) cannot be determined at makefile read time, perhaps you should do:
// get a list of expected output files:
PDF_SOURCES:=$(wildcard source/pdf/*)
all: .do_fix
#echo done
$(BUILDDIR)/pdf:
mkdir -p $#
.do_sphynx: $(PDF_SOURCES) | $(BUILDDIR)/pdf
$(SPHINXBUILD) -b pdf $(ALLSPHINXOPTS) source/pdf/ $(BUILDDIR)/pdf_broken
touch $#
.do_fix: .do_sphynx
#for src in $$(ls source/pdf/*.pdf); do \
trg=$${src/#"source/pdf"/"$(BUILD_DIR)/pdf"}; \
[[ $$src -nt $$trg ]] && \
echo "$$src ==> $$trg" && pdftk $$src output $$trg; \
done
touch $#
One note -- the -nt comparator in the if will return true if $trg does not exist, so it will cover the case where the file is missing, or the target is older than the source. Again not tested, but it should work.
I have a script which begins by defining a series of variables, before running a programme with those variables. However, the script is being rejected from Grid Engine (it works on a workstation, but as one component of an array job, it needs to run via SGE) because the variables are being read as commands, resulting in a "Command not found" response.
The error is completely reproduced using the following:
#!/bin/bash
#$ -M not.real#email.address
#$ -m be
#$ -o /scratch/MScGWAS/Output
#$ -e /scratch/MScGWAS/Errors
#$ -q long.q
#$ -cwd
CHR=$1
CHUNK_START=`printf "%.0f" $2`
CHUNK_END=`printf "%.0f" $3`
Output Example:
CHR=1: Command not found.
CHUNK_START=1: Command not found.
CHUNK_END=5000000: Command not found.
How can I get GridEngine to use bash as the interpreter for this script?
You are not executing your script with bash, but with a different shell (e.g. tcsh).
It sounds like your grid engine cluster is configured with the queues in posix_compliant mode and /bin/csh as the default shell. In posix_compliant mode the initial #! is ignored and you need to specify the shell via a command line switch or with a suitable #$ directive.
Adding the following line to your script should work:
#$ -S /bin/bash