For a Hello world uboot project I am using this tutorial.
I have used GNU ARM toolchain
Downloaded Uboot source : u-boot-2017.09
Compiled it
make vexpress_ca9x4_defconfig ARCH=arm CROSS_COMPILE=../gcc-arm-none-eabi-6-2017-q2-update/bin/arm-none-eabi-
make all ARCH=arm CROSS_COMPILE=../gcc-arm-none-eabi-6-2017-q2-update/bin/arm-none-eabi-
And the hello world project looks like
test.c
volatile unsigned int * const UART0DR = (unsigned int *)0x101f1000;
void print_uart0(const char *s) {
while(*s != '\0') { /* Loop until end of string */
*UART0DR = (unsigned int)(*s); /* Transmit char */
s++; /* Next char */
}
}
void c_entry() {
print_uart0("Hello world!\n");
}
startup.s
.global _Reset
_Reset:
LDR sp, =stack_top
BL c_entry
B .
test.ld
ENTRY(_Reset)
SECTIONS
{
. = 0x100000; /*initial address*/
.startup . : { startup.o(.text) }
.text : { *(.text) }
.data : { *(.data) }
.bss : { *(.bss COMMON) }
. = ALIGN(8);
. = . + 0x1000; /* 4kB of stack memory */
stack_top = .;
}
And the compilation
../gcc-arm-none-eabi-6-2017-q2-update/bin/arm-none-eabi-gcc -c -mcpu=arm926ej-s test.c -o test.o
../gcc-arm-none-eabi-6-2017-q2-update/bin/arm-none-eabi-as -mcpu=arm926ej-s startup.s -o startup.o
../gcc-arm-none-eabi-6-2017-q2-update/bin/arm-none-eabi-ld -T test.ld -Map=test.map test.o startup.o -o test.elf
../gcc-arm-none-eabi-6-2017-q2-update/bin/arm-none-eabi-objcopy -O binary test.elf test.bin
Create Image :
mkimage -A arm -C none -O linux -T kernel -d test.bin -a 0x00100000 -e 0x00100000 test.uimg
Output :
Image Name:
Created: Mon Oct 23 20:58:01 2017
Image Type: ARM Linux Kernel Image (uncompressed)
Data Size: 146 Bytes = 0.14 kB = 0.00 MB
Load Address: 00100000
Entry Point: 00100000
Create a single binary :
cat ../u-boot-2017.09/u-boot test.uimg > flash.bin
Calculated uboot binary size
printf "bootm 0x%X\n" $(expr $(stat -c%s u-boot.bin) + 65536)
bootm 0x218F20
Then run :
qemu-system-arm -M vexpress-a9 -kernel flash.bin -m 128M -nographic
Interrupted it and then run bootm 0x218F20
But it says
Wrong Image Format for bootm command
ERROR: can't get kernel image!
Any suggestion?
Either try go command with same built image (go 0x218F20) Or to use bootm
refer [1] (5.12.3. Processor cache considerations), the mkimage command seems to be wrong.
[1] https://www.denx.de/wiki/DULG/UBootStandalone
Related
I'm using nextflow to analyse minION data. Blast+ terminates with error exit status (2), Command exit status:2 and Command output: (empty)
-HP-Z6-G4-Workstation:~/nextflow_pipelines/nf_pipeline/20221025_insect$ nextflow cat_working_nextflow.nf
N E X T F L O W ~ version 22.04.5
Launching `cat_working_nextflow.nf` [admiring_hopper] DSL1 - revision: 2916bc12af
executor > local (78)
[38/2d0584] process > concatinate (AIG363_pass_barcode01_0eb3c2c3_2.fastq) [100%] 38 of 38 ✔
[dd/3cabdf] process > fastqconvert (output.fastq) [100%] 38 of 38 ✔
[47/dab2cd] process > blast_raw (insect.fasta) [ 0%] 0 of 38
executor > local (78)
[38/2d0584] process > concatinate (AIG363_pass_barcode01_0eb3c2c3_2.fastq) [100%] 38 of 38 ✔
[dd/3cabdf] process > fastqconvert (output.fastq) [100%] 38 of 38 ✔
[47/dab2cd] process > blast_raw (insect.fasta) [ 2%] 1 of 37, failed: 1
Error executing process > 'blast_raw (insect.fasta)'
Caused by:
Process `blast_raw (insect.fasta)` terminated with an error exit status (2)
Command executed:
blastn -query insect.fasta -db /home/blast/nt_db_20221011/nt -outfmt 11 -out blastrawreads.asn -evalue 0.1 -numgnments 1
blast_formatter blastr-archive blastrawreads.asn awrea-outfmt 5 -out blastrawreads.xml
blast_formatter -archive blastrawreads.asn -outfmt "6 qaccver saccver pident length evalue bitscore stitle" -out blastrawreads_rt.tsv
sort -n -r -k 6 blastrawreads_unsort.tsv > blastrawreads.tsv
Command exit status:
2
Command output:
(empty)
Command error:
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: No alias or index file found for nucleotide database [/home/blast/nt_db_20221011/nt] in search path [/home/shaextflow_pipelines/nf_pipeline/20221025_insect/work/96/e885b7e53e1bcf30e33526265e9a3c::]
Work dir:
/home/nextflow_pipelines/nf_pipeline/20221025_insect/work/96/e885b7e53e1bcf30e33526265e9a3c
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
The nf file:
\#!/usr/bin/env nextflow
//data_location
params.outdir = './results'
params.in = "$PWD/\*.fastq"
dataset = Channel.fromPath(params.in)
params.db = "/home/blast/nt_db_20221011/nt"
process concatenate {
tag "$x"
publishDir "${params.outdir}", mode:'copy'
input:
path (x) from dataset
output:
path ("output.fastq") into cat_ch
script:
"""
cat $x > output.fastq
"""
}
process fastqconvert {
tag "$y"
publishDir "${params.outdir}", mode:'copy'
input:
path (y) from cat_ch
output:
path ("insect.fasta") into convert1_ch,convert2_ch,convert3_ch
script:
"""
seqtk seq -a $y > insect.fasta
"""
}
process blast_raw {
tag "$z"
publishDir "${params.outdir}", mode:'copy'
input:
path (z) from convert1_ch
output:
path ('blastrawreads.xml') into blastrawreads_xml_ch
script:
"""
blastn \
-query $z -db ${params.db} \
-outfmt 11 -out blastrawreads.asn \
-evalue 0.1 \
-num_alignments 1 \
blast_formatter \
-archive blastrawreads.asn \
-outfmt 5 -out blastrawreads.xml
blast_formatter \
-archive blastrawreads.asn \
-outfmt "6 qaccver saccver pident length evalue bitscore stitle" -out blastrawreads_unsort.tsv
sort -n -r -k 6 blastrawreads_unsort.tsv > blastrawreads.tsv
"""
}
I can see that the insect.fasta file has been produced and has the appropriate permissions and is located in the expected dir.
I used the following command to download the nt database
update_blastdb.pl --decompress nt --passive --source gcp
gcp is the google cloud in Australia
The nt database is ~26GiG in size.
I really need an excel, asn and fasta file from blast results for downstream analysis.
Any help would be much appreciated.
BLAST Database error: No alias or index file found for nucleotide
database [/home/blast/nt_db_20221011/nt]
I think you should be able to re-create the above error independently of Nextflow using:
blastdbcmd -db /home/blast/nt_db_20221011/nt -info
Note that the db argument must be a dbname, not a path. For /home/blast/nt_db_20221011/nt to work correctly, you should be able to list your db files using: ls /home/blast/nt_db_20221011/nt.*
Not sure if there's a typo in your question, but the size of the nt database is about an order of magnitude larger, at approximately 250G. I wonder if simply re-downloading the database fixes the problem? Note that you can get a list of BLAST databases (showing their sizes and dates last updated) using:
update_blastdb.pl --showall pretty --source gcp
Note also that DSL1 is now end-of-life1 and will be removed going forward. I strongly recommend migrating to using DSL2 syntax when you get a chance.
From the comments:
The problem is that when you use params to specify a path, the path or files specified will not be localized inside the process working directory when the task is run. What you want is just a second input (value) channel. For example, using DSL2 syntax:
params.db = "/home/blast/Geminiviridae_db_20221118/geminiviridae"
process blast_raw {
tag { query_fasta }
input:
path query_fasta
path db
output:
path "geminiviridae.xml"
"""
blastn \\
-query "${query_fasta}" \\
-db "${db}" \\
-max_target_seqs 10 \\
-outfmt 5 \\
-out "geminiviridae.xml"
"""
}
workflow {
db = file( params.db )
blast_raw( your_upstream_ch, db)
}
I want to link my program with the static version of cublas, but I get some undefined references. The command and error are
$ nvcc test.cu -o test --cudart=static -ldl -lpthread -lcurand_static -lcublas_static -lculibos
/home/mahmood/cuda_10.1.168/bin/../targets/x86_64-linux/lib/libcublas_static.a(cublas.o): In function `cublasCtxInit(cublasContext**)':
cublas.compute_75.cudafe1.cpp:(.text+0x34b): undefined reference to `cublasLtCtxInit'
cublas.compute_75.cudafe1.cpp:(.text+0x417): undefined reference to `init_gemm_select'
...
...
In fact, the library path is fine and the cublasLtCtxInit exists in the static library file.
$ ls -l /home/mahmood/cuda_10.1.168/lib64/libcublas_static.a
-rw-rw-r-- 1 mahmood mahmood 75127082 Jun 27 16:06 /home/mahmood/cuda_10.1.168/lib64/libcublas_static.a
$ grep cublasLtCtxInit ~/cuda_10.1.168/lib64/libcublas_static.a
Binary file /home/mahmood/cuda_10.1.168/lib64/libcublas_static.a matches
$ echo $LD_LIBRARY_PATH
/home/mahmood/cuda_10.1.168/lib64:
So, how can I fix that?
The correct static linking sequence with cublas can be found in the Makefile for the conjugateGradient CUDA sample code.
The needed switches for nvcc are:
-lcublas_static -lcublasLt_static -lculibos
example:
$ cat t1752.cu
#include <cublas_v2.h>
int main(){
cublasHandle_t h;
cublasCreate(&h);
}
$ nvcc t1752.cu -o t1752 -lcublas_static -lcublasLt_static -lculibos
$
I have a problem with my C project built under Debian Jessie. After doing some stuffs now I need to work with MySQL so i download the library and try to update my Makefile.
This is my Makefile right now
CC = gcc
CFLAGS = -Wall -Wextra
LDFLAGS = -lbluetooth -lpthread -lmysqlclient
LFLAGS = -lm
INC = -I/usr/include/mysql
SOURCES = stb.c btscan.c and.c gima.c database.c
OBJECTS = $(SOURCES:.c=.o)
EXECUTABLE = stb
$(EXECUTABLE): $(OBJECTS)
$(CC) $(CFLAGS) $(OBJECTS) -o $# $(LFLAGS) $(LDFLAGS)
stb.o: btscan.h and.h gima.h database.h
btscan.o: btscan.h
and.o: and.h
gima.o: gima.h
database.o: database.h
clean:
#rm -f *.o *.out stb
and this is the files where I want to use the library
stb.c
#include "btscan.h"
#include "and.h"
#include "gima.h"
#include "database.h"
struct device* bt_devices;
struct device* ble_devices;
int main(void) {
//-------------------------------- DATABASE CONNECTION ----------------
//MYSQL *con = mysql_init(NULL);
....... }
and finally database.h
#ifndef _DATABASE_H
#define _DATABASE_H
#include <my_global.h>
#include <mysql.h>
#endif
When I try to make i receive "Fatal error : my_global.h No such file or directory". However if i try MySQL on a single test file and compiling it with
gcc -o test test.c -I/usr/include/mysql -lmysqlclient
it works. Where I made a mistake?
Thanks in advance
If you'd shown us the output of the compiler, or examine it yourself, you'll immediately see that what you're running on the command line is not the same at all as what make is running: in particular make is not adding the -I/usr/include/mysql flag to the command line.
That's because in your makefile you set:
INC = -I/usr/include/mysql
but nowhere in your makefile (as you've shown it) is the variable INC actually used, so this is essentially a no-op.
Since you're using the standard GNU make compilation rules, you should be setting standard GNU make variables:
CPPFLAGS = -I/usr/include/mysql
I have a Tcl code that is being sourced from a C application using:
Tcl_Eval(tcl_interp, "source nmsp.tcl")
Everything runs fine.
However, the namespace scope isn't preserved. For example, the following file:
#!/bin/sh
# namespace evaluation
namespace eval bob {
namespace eval joe {
proc proc1 {} {}
}
proc proc2 {} {
puts "proc2"
}
proc ::proc3 {} {
puts "proc3"
}
proc joe::proc4 {} {
puts "proc4"
}
}
puts "Namespace calling [info procs ::bob\::*]"
when run by itself will produce this output:
Namespace calling ::bob::proc2
But when sourcing from Tcl_Eval will not print anything. In fact, the proc2 procedure can be called by itself fine without any namespace designation.
Anyone knows what may be causing it? I really like the encapsulation that namespaces provide.
Seems fine to me.
I created the following Tcl extension to perform your Tcl_Eval:
#include <tcl.h>
static int
DotestCmd(ClientData clientData, Tcl_Interp *interp,
int objc, Tcl_Obj *const objv[])
{
return Tcl_Eval(interp, "source test_namespace.tcl");
}
int DLLEXPORT
Testnamespace_Init(Tcl_Interp *interp)
{
if (Tcl_InitStubs(interp, "8.4", 0) == NULL) {
return TCL_ERROR;
}
Tcl_CreateObjCommand(interp, "dotest", DotestCmd, NULL, NULL);
return Tcl_PkgProvide(interp, "testnamespace", "1.0");
}
Being on windows, I compiled this using:
cl -nologo -W3 -O2 -MD -DNDEBUG -DUSE_TCL_STUBS -I\opt\tcl\include -c test_namespace.c
link -dll -release -out:testnamespace.dll test_namespace.obj \opt\tcl\lib\tclstub85.lib
and then created a test_namespace.tcl file with the content you posted above. Running this produces the following:
C:\opt\tcl\src>tclsh
% load testnamespace.dll Testnamespace
% dotest
Namespace calling ::bob::proc2
%
and further introspection shows things are as I would expect from that script:
% namespace children ::
::platform ::activestate ::bob ::tcl
% namespace children ::bob
::bob::joe
%
You probably are doing something weird in your C code first if this is really not working for you.
Update
The above example is for extending tcl with a compiled package. Apparently the OP is embedding Tcl into some other application. A trivial example of doing this is provided here which also runs the same command to the same effect as above. In reality when embedding Tcl into an application the code should use the tclAppInit.c file and provide its own Tcl_AppInit function. By running the usual Tcl_Main you get the full capabilities for processing events (needed for fileevents or after commands) and the interactive shell. An example of that follows the trivial version:
/* trivial embedding Tcl example */
#include <tcl.h>
#include <locale.h>
int
main(int argc, char *argv[])
{
Tcl_Interp *interp = NULL;
int r = TCL_ERROR;
setlocale(LC_ALL, "C");
interp = Tcl_CreateInterp();
if (interp != NULL) {
Tcl_FindExecutable(argv[0]);
r = Tcl_Eval(interp, "source test_namespace.tcl");
if (TCL_OK == r)
r = Tcl_Eval(interp, "puts [namespace children ::bob]");
Tcl_DeleteInterp(interp);
}
return r;
}
Running the above:
C:\opt\tcl\src>cl -nologo -W3 -O2 -MD -I\opt\tcl\include test_namesp_embed.c -link -subsystem:console -release -libpath:\opt\tcl\lib tcl85.lib
test_namesp_embed.c
C:\opt\tcl\src>test_namesp_embed.exe test_namespace.tcl
Namespace calling ::bob::proc2
::bob::joe
A better embedding scheme that uses tclAppInit to extend a stock Tcl interpreter:
#include <tcl.h>
#include <locale.h>
#define TCL_LOCAL_APPINIT Custom_AppInit
int
Custom_AppInit(Tcl_Interp *interp)
{
return Tcl_Eval(interp, "source test_namespace.tcl");
}
#include "/opt/tcl/src/tcl.git/win/tclAppInit.c"
Building and running this also produces the same output as previous versions:
C:\opt\tcl\src>cl -nologo -W3 -O2 -MD -I\opt\tcl\include test_namesp_embed.c -link -subsystem:console -release -libpath:\opt\tcl\lib tcl85.lib
C:\opt\tcl\src>test_namesp_embed.exe
Namespace calling ::bob::proc2
% namespace children ::bob
::bob::joe
% exit
As far as I'm aware, the only way your code could not produce the message you expect is if the current namespace at the point it was called was other than the global namespace. Suppose the current namespace was ::foo, the first namespace eval would work in ::foo::bob and the inner one in ::foo::bob::joe. Unqualified procedure definitions put their definitions in the current namespace, of course.
To detect if this is really the case, add the output of the namespace current command to your printed message.
If this is the problem, change the outer namespace eval to use a fully-qualified name:
namespace eval ::bob { # <<<<<<< NOTE THIS HERE!
namespace eval joe {
proc proc1 {} {}
}
proc proc2 {} {
puts "proc2"
}
proc ::proc3 {} {
puts "proc3"
}
proc joe::proc4 {} {
puts "proc4"
}
}
If you're writing a Tcl package this is very strongly recommended and it is a good idea even if you're not going all the way to that extent; you can never be quite sure what context a script is going to be sourced in. (The inner namespace eval is OK though; that's running inside a known context, the outer namespace eval.)
Sorry guys for trouble. I found the problem.
The problem is in my code. I had the following procedure which I completely forgot about:
rename proc _proc
_proc proc {name args body} {
global pass_log_trace
set g_log_trace "0"
if {[info exists pass_log_trace]} {
set g_log_trace $pass_log_trace
}
# simple check if we have double declaration of the same procedure
if {[info procs $name] != ""} {
puts "\nERROR: redeclaration of procedure: $name"
}
_proc $name $args $body
if {$g_log_trace != 0} {
trace add execution $name enter trace_report_enter
trace add execution $name leave trace_report_leave
}
}
The purpose of this procedure, mainly, is to add entry and exit point tracers to all the procedures in my code. For some reason, which I'm still investigating, it also removes the namespace scoping.
How do you traverse a directory tree in your favorite language?
What do you need to know to traverse a directory tree in different operating systems? On different filesystems?
What's your favorite library/module for aiding in traversing a directory tree?
In Python:
If you're looking for a quick, clean, and portable solution try:
import os
base_dir = '.'
def foo(arg, curr_dir, files):
print curr_dir
print files
os.path.walk(base_dir, foo, None)
Note that you can modify foo to do something else instead of just printing the names. Furthermore, if you're interested in migrating to Python 3.0, you will have to use os.walk() instead.
In Java:
Recursion is useful here. Following is a Java code snippet that's been all over the Internet for ages. Not sure who deserves the credit for it.
// Process all files and directories under dir
public static void visitAllDirsAndFiles(File dir) {
process(dir); //do something useful with the file or dir
if (dir.isDirectory()) {
String[] children = dir.list();
for (int i=0; i<children.length; i++) {
visitAllDirsAndFiles(new File(dir, children[i]));
}
}
}
bash:
#!/bin/bash
function walk_tree {
echo "Directory: $1"
local directory="$1"
local i
for i in "$directory"/*;
do
echo "File: $i"
if [ "$i" = . -o "$i" = .. ]; then
continue
elif [ -d "$i" ]; then # Process directory and / or walk-down into directory
# add command here to process all files in directory (i.e. ls -l "$i/"*)
walk_tree "$i" # DO NOT COMMENT OUT THIS LINE!!
else
continue # replace continue to process individual file (i.e. echo "$i")
fi
done
}
walk_tree $HOME
(adapted from http://ubuntuforums.org/showthread.php?t=886272 Comment #4)
In C#:
Stack<DirectoryInfo> dirs = new Stack<DirectoryInfo>();
dirs.Push(new DirectoryInfo("C:\\"));
while (dirs.Count > 0) {
DirectoryInfo current = dirs.Pop();
// Do something with 'current' (if you want)
Array.ForEach(current.GetFiles(), delegate(FileInfo f)
{
// Do something with 'f'
});
Array.ForEach(current.GetDirectories(), delegate(DirectoryInfo d)
{
dirs.Push(d);
});
}
C++
#include <utility>
#include <boost/filesystem.hpp>
#include <boost/foreach.hpp>
#define foreach BOOST_FOREACH
namespace fs = boost::filesystem;
fs::recursive_directory_iterator it(top), eod;
foreach (fs::path const & p, std::make_pair(it, eod)) {
if (is_directory(p)) {
...
} else if (is_regular_file(p)) {
...
} else if (is_symlink(p)) {
...
}
}
On Linux with GNU tools
find -print0 | xargs -0 md5sum
or
find -print0 | xargs -0 -iASD echo 'this file "ASD" should be dealt with lile this (ASD)'
mmmm, C# with a dose of recursion.....
public static List<string> CrawlPath(string path, bool IncludeSubFolders)
{
List<string> fileList = new List<string>();
try
{
Stack<string> filez = new Stack<string>(Directory.GetFiles(path));
while (filez.Count > 0)
{
fileList.Add(filez.Pop());
}
if (IncludeSubFolders)
{
filez = new Stack<string>(Directory.GetDirectories(path));
while (filez.Count > 0)
{
string curDir = filez.Pop();
fileList.AddRange(CrawlPath(curDir, IncludeSubFolders));
}
}
}
catch (System.Exception err)
{
Console.WriteLine("Error: " + err.Message);
}
return fileList;
}