I am currently experiencing a really strange bug when compiling for u-boot:
The vector
init_fnc_t *init_sequence[] ={...}
is filled with 0's / NULLs instead of function pointers. I thought I outsmarted the compiler by calling all those functions 'by hand'. However this bug has even more ramifications as the driver struct also gets 0 / NULL pointers:
static struct serial_device my_serial_drv = {
.name = "my_serial",
.start = my_serial_init,
.stop = NULL,
.setbrg = my_serial_setbrg,
.putc = my_serial_putc,
.puts = my_serial_puts,
.getc = my_serial_getc,
.tstc = my_serial_tstc,
};
which, of course, when I call
'my_serial_drv'->start();
sets the pc to 0 and subsequently crashes everything.
Fun fact: the .name reaches the binary, so the .data sections are probably fine once they are set.
I have tested this with aarch64-linux-gnu-*-4.7 and aarch64-linux-gnu-*-4.9 binaries.
You can find 4.9 from:
http://releases.linaro.org/latest/components/toolchain/binaries.
Any help would be greatly appreciated :)
The u-boot.bin file seems allright. After investigating why this works I saw that u-boot's make is running a separate command to fix the bin:
start=$(aarch64-linux-gnu-nm u-boot | grep __rel_dyn_start | cut -f 1 -d ' ');
end=$(aarch64-linux-gnu-nm u-boot | grep __rel_dyn_end | cut -f 1 -d ' ');
tools/relocate-rela u-boot.bin 0x3e900000 $start $end
(these were a single line but I split it for readability )
Related
I'd like to add a new option to ntpd however I couldn't find how to generate ntpd/ntpd-opts{.c, .h} after adding some lines to ntpd/ntpdbase-opts.def e.g.,
$ git diff ntpd/ntpdbase-opts.def
diff --git a/ntpd/ntpdbase-opts.def b/ntpd/ntpdbase-opts.def
index 66b953528..a790cbd51 100644
--- a/ntpd/ntpdbase-opts.def
+++ b/ntpd/ntpdbase-opts.def
## -479,3 +479,13 ## flag = {
the server to be discovered via mDNS client lookup.
_EndOfDoc_;
};
+
+flag = {
+ name = foo;
+ value = F;
+ arg-type = number;
+ descrip = "Some new option";
+ doc = <<- _EndOfDoc_
+ For testing purpose only.
+ _EndOfDoc_;
+};
Do you have any ideas?
how to generate ntpd/ntpd-opts{.c, .h} after adding some lines to ntpd/ntpdbase-opts.def
It is just in build scripts. Just compile https://github.com/ntp-project/ntp/blob/master-no-authorname/INSTALL#L30 it normally and make will pick it up.
https://github.com/ntp-project/ntp/blob/master-no-authorname/ntpd/Makefile.am#L304
https://github.com/ntp-project/ntp/blob/master-no-authorname/ntpd/Makefile.am#L183
In addition to #KamilCuk's answer, we need to do the following to add custom options:
Edit *.def file
Run bootstrap script
Run configure script with --disable-local-libopts option
Run make
For example,
$ git diff ntpd/ntpdbase-opts.def
diff --git a/ntpd/ntpdbase-opts.def b/ntpd/ntpdbase-opts.def
index 66b953528..a790cbd51 100644
--- a/ntpd/ntpdbase-opts.def
+++ b/ntpd/ntpdbase-opts.def
## -479,3 +479,13 ## flag = {
the server to be discovered via mDNS client lookup.
_EndOfDoc_;
};
+
+flag = {
+ name = foo;
+ value = F;
+ arg-type = number;
+ descrip = "Some new option";
+ doc = <<- _EndOfDoc_
+ For testing purpose only.
+ _EndOfDoc_;
+};
This change yields:
$ ./ntpd --help
ntpd - NTP daemon program - Ver. 4.2.8p15
Usage: ntpd [ -<flag> [<val>] | --<name>[{=| }<val>] ]... \
[ <server1> ... <serverN> ]
Flg Arg Option-Name Description
-4 no ipv4 Force IPv4 DNS name resolution
- prohibits the option 'ipv6'
...
-F Num foo Some new option
opt version output version information and exit
-? no help display extended usage information and exit
-! no more-help extended usage information passed thru pager
Options are specified by doubled hyphens and their name or by a single
hyphen and the flag character.
...
I am performing a scatter-gather operation on NextFlow.
It looks like the following:
reads = PATH+"test_1.fq"
outdir = "results"
split_read_ch = channel.fromFilePairs(reads, checkIfExists: true, flat:true ).splitFastq( by: 10, file:"test_split" )
process Scatter_fastP {
tag 'Scatter_fastP'
publishDir outdir
input:
tuple val(name), path(reads) from split_read_ch
output:
file "${reads}.trimmed.fastq" into gather_fatsp_ch
script:
"""
fastp -i ${reads} -o ${reads}.trimmed.fastq
"""
}
gather_fatsp_ch.collectFile().view().println{ it.text }
I run this code with all the benchmarks options proposed by Nextflow (https://www.nextflow.io/docs/latest/tracing.html):
nextflow run main.nf -with-report nextflow_report -with-trace nextflow_trace -with-timeline nextflow_timeline -with-dag nextflow_dag.html
In these tracing files, I can find the resources and speed of the 10 Scatter_fastP processes.
But I would like to also measure the resources and speed of the creation of the split_read_ch and the gather_fastp_ch channels.
I have tried to include the channels' creation in processes but I cannot find a solution to make it work.
Is there a way to include the channel creation into the tracing files? Or is there a way I have not found to create these channels into processes?
Thank you in advance for your help.
Although Nextflow can parse FASTQ files and split them into smaller files etc, generally it's better to pass off these operations to another process or set of processes, especially if your input FASTQ files are large. This is beneficial in two ways: (1) your main nextflow process doesn't need to work as hard, and (2) you get granular task process stats in your nextflow reports.
The following example uses GNU split to split the input FASTQ files, and gathers the outputs using the groupTuple() operator and the groupKey() built-in to stream the collected values as soon as possible. You'll need to adapt for your non-gzipped inputs:
nextflow.enable.dsl=2
params.num_lines = 40000
params.suffix_length = 5
process split_fastq {
input:
tuple val(name), path(fastq)
output:
tuple val(name), path("${name}-${/[0-9]/*params.suffix_length}.fastq.gz")
shell:
'''
zcat "!{fastq}" | split \\
-a "!{params.suffix_length}" \\
-d \\
-l "!{params.num_lines}" \\
--filter='gzip > ${FILE}.fastq.gz' \\
- \\
"!{name}-"
'''
}
process fastp {
input:
tuple val(name), path(fastq)
output:
tuple val(name), path("${fastq.getBaseName(2)}.trimmed.fastq.gz")
"""
fastp -i "${fastq}" -o "${fastq.getBaseName(2)}.trimmed.fastq.gz"
"""
}
workflow {
Channel.fromFilePairs( './data/*.fastq.gz', size: 1 ) \
| split_fastq \
| map { name, fastq -> tuple( groupKey(name, fastq.size()), fastq ) } \
| transpose() \
| fastp \
| groupTuple() \
| map { key, fastqs -> tuple( key.toString(), fastqs ) } \
| view()
}
I have a script where I have multiple folders each with three audio files in them ID#_1, ID#_2, and ID#_3. The user can input a string of different ID#s, one after the other, and then the script recognizes the different IDs and runs the code for each of them.
I have a for loop set up for this -
form Settings
comment Enter the IDs of the different subjects
sentence subjectIDs
endform
numOfSubjects = length(subjectIDs$)/4
for i from 0 to (numOfSubjects - 1)
subjectID$ = mid$(subjectIDs$, 1 + 4*i, 4 + 4*i)
outFile$ = subjectID$ + "/SubjectResponseOnsets" + subjectID$ + ".txt"
path$ = subjectID$ + "/" + subjectID$
#firstOutput
#secondOutput
#thirdOutput'
Each of these procedures is defined previously in the code, and they basically output certain ranges from the audio files out to a text file.
The code seems to work fine and generate the output file correctly when one ID is given, but when I try to run it with more than one ID at a time, only the text file for the first ID is outputted.
The for loop does not seem to be working well, but the code does work fine in the first run.
I would greatly appreciate any help!
I don't know if I understood well what your script was trying to do, since the snippet you pasted was incomplete. It's best if you provide code that is executable as is. In this case, you were missing the closing endfor, and you were calling some procedures that were not defined in your snippet (not even as placeholders). I had to write some dummy procedures just to make it run.
Since you also didn't say how your script was failing, it was unclear what needed to be fixed. So I took a stab at making it work.
It sounded as if your ID splitting code was giving you some problems. I took the split procedure from the utils plugin available through CPrAN, which makes inputting the IDs easier (full disclosure: I wrote that plugin).
form Settings
comment Enter the IDs of the different subjects
sentence subjectIDs 01 02 03
endform
#split: " ", subjectIDs$
numOfSubjects = split.length
for i to numOfSubjects
subjectID$ = split.return$[i]
path$ = subjectID$
outFile$ = path$ + "/SubjectResponseOnsets" + subjectID$ + ".txt"
# Make sure output directory exists
createDirectory: path$
#firstOutput
#secondOutput
#thirdOutput
endfor
procedure firstOutput ()
appendFileLine: outFile$, "First"
endproc
procedure secondOutput ()
appendFileLine: outFile$, "Second"
endproc
procedure thirdOutput ()
appendFileLine: outFile$, "Third"
endproc
# split procedure from the utils CPrAN plugin
# http://cpran.net/plugins/utils
procedure split (.sep$, .str$)
.seplen = length(.sep$)
.length = 0
repeat
.strlen = length(.str$)
.sep = index(.str$, .sep$)
if .sep > 0
.part$ = left$(.str$, .sep-1)
.str$ = mid$(.str$, .sep+.seplen, .strlen)
else
.part$ = .str$
endif
.length = .length+1
.return$[.length] = .part$
until .sep = 0
endproc
If this is not what you are having trouble with, you'll have to be more specific.
I'm running a process, which uses a set of parameters defined in a file parameters.py
Now, I'd like to swept the value of one of the parameters over certain range. Thus, I wrote a batch file to automatise the procedure.
Problem
My problem is that I need to modify the 20th line of the file parameter, from value = 200 to value = $VAR, where $VAR sets the new value of the parameter.
Question
Is there a bash command that allows to change a specific target line of the file?
Thank you and cheers.
Try doing this with sed :
sed -i "20s/value = 200/value = $VAR/" file.txt
That will change value = 200 to value = $VAR on line 20. s/// is a skeleton for sed substitutions : s/before/after/
The -i switch edit the file in place
While it's certainly possible, I wouldn't recommend it. One day, someone will add a comment before this line or an empty line and your script will break.
Use sed instead:
sed -e 's/value = 200/value = $VAR/' < parameters.py
An even better solution would be to move everything in parameters.py into parameterdefaults.py like so:
parameterdefaults.py:
options = {
"value": 200,
}
parameters.py:
import parameterdefaults
options = dict( **parameterdefaults.options ) # copy defaults
options['value'] = 10 # Override the few values you need to change
or even better:
codethatneedsparameters.py:
import parameterdefaults
import parameters
options = dict( **parameterdefaults.options ) # copy defaults
options.update( parameters.options ) # merge with changes
Now you can write:
parameters.py:
options = {
"value": 10,
}
The easiest way (but not the best) to do this instead of hacking the script is to change it from
value = 200
to
import os # somewhere at the top if need be.
value = int(os.environ.get('VAR', 200))
That way it can be modified from the calling process what ever that may be.
I'm trying to make a simple Vim script that would create very compact top-level folds for c files. Ideally, if it was run on this code:
static void funca(...)
{
...
}
/* Example comment */
static void funcb(...)
{
...
}
Then it would create folds which would look like this when closed:
+-- x Lines: static void funca(...)----------------------
+-- x Lines: static void funcb(...)----------------------
So basically it would be like foldmethod=syntax with foldlevel=1, except that each fold would start one line further up, and would extend further down to include all following blank lines.
I know how to make one of these folds (assuming foldmethod=manual):
/^{<cr>kVnn?^$<cr>zf
But I'm not sure how to put it into a function. This is my effort:
function Cfold()
set foldmethod=manual " Manual folds
ggzE " Delete all folds
while (/^{<cr>) " Somehow loop through each match
kVnn?^$<cr>zf " This would work fine except for the last function
endwhile
endfunction
map <Leader>f :call Cfold()<cr>
But it isn't valid, I'm not entirely sure how functions work. Also, it won't work for the last function in the file, since it won't find '^{' again. If someone could help me get this working, and somehow add a case for the last function in a file, I would be extremely grateful.
Thanks in advance :)
You can create folds programmatically using the foldexpr and foldtext. Try this, though you may have to tweak CFoldLevel so it doesn't swallow non-function parts of the code:
function! CFoldLevel(lnum)
let line = getline(a:lnum)
if line =~ '^/\*'
return '>1' " A new fold of level 1 starts here.
else
return '1' " This line has a foldlevel of 1.
endif
endfunction
function! CFoldText()
" Look through all of the folded text for the function signature.
let signature = ''
let i = v:foldstart
while signature == '' && i < v:foldend
let line = getline(i)
if line =~ '\w\+(.*)$'
let signature = line
endif
let i = i + 1
endwhile
" Return what the fold should show when folded.
return '+-- ' . (v:foldend - v:foldstart) . ' Lines: ' . signature . ' '
endfunction
function! CFold()
set foldenable
set foldlevel=0
set foldmethod=expr
set foldexpr=CFoldLevel(v:lnum)
set foldtext=CFoldText()
set foldnestmax=1
endfunction
See :help 'foldexpr' for more details.