The programs run with gem5 before are all without parameters. But what should I do if the program I am running requires parameters. I tried --cmd="add 3 4"， which is not work. I am currently trying to run Coremark with gem5. The command to run Coremark directly is ./coremark.exe 0x0 0x0 0x66 0 7 1 2000> ./run1.log.
You can pass command line parameters with --options as in:
gem5.opt configs/example/se.py --cmd add --options '3 4'
Related
I'm trying to use the full system to do some experiments.
I used the boot-exit image and vmlinux-5.4.49 provided by this website（https://gem5art.readthedocs.io/en/latest/tutorials/boot-tutorial.html）
I first tried using the terminal script that comes with gem5.
In one of the terminals I execute:
/build/X86/gem5.opt
configs/example/fs.py \
--kernel=../../full_system_image/binaries/vmlinux-4.19.83 \
--disk-image=../../full_system_image/disks/boot-exit.img "
I execute in another terminal:
util/term/m5term localhost 3456
After that, I successfully entered, although I waited for dozens of minutes.
I can enter commands normally.
.
But i want to run my program. I don't want to have to enter the terminal every time, that would be too slow.
For boot-exit images:
I added/root/init.sh instruction at the end of /root/.bashrc file. In this way, the init.sh script will be executed every time the system is entered.
The content of the init.sh file is:
m5 readfile > /tmp/run.sh
/bin/sh /tmp/run.sh
m5 exit
I added run_hello.sh and hello executable files (output hello, world) in the /root directory.
The content of the run_hello.sh file is:
m5 resetstats
/root/hello > /tmp/hello.out
m5 dumpstats
I executed the following command:
/usr/local/src/gem5/build/X86/gem5.opt --debug-flags=CacheAll --debug-file=/usr/local/src/gem5/runScripts/attack_spectre/trace2.out /usr/local/src/gem5/configs/example/fs.py --kernel=../../full_system_image/binaries/vmlinux-4.19.83 --disk-image=../../full_system_image/disks/boot-exit.img --l1d_replacement=LRU --mem-size=4GB --l1d_size=32kB --l1d_assoc=8 --l1i_size=32kB --l1i_assoc=4 --l2_assoc=16 --l2_size=2MB --caches --l2cache --cpu-type=DerivO3CPU --script=/root/run_hello.sh
The process will always be stuck here.
It seems to keep waiting for a terminal connection.
If I don't connect, it just waits until. When I connect( util/term/m5term localhost 3456), it will show that there is a terminal connected.
When I type m5 exit in the connected terminal, it ends on both sides.
What should I do to run my code without connecting to a terminal?
thank you very much! ! !
I am trying to run gem5 in FS mode by using command as : "build/ARM/gem5.opt configs/example/fs.py --disk-image=/home/coep/gem5%202/full_system_images/aarch32-ubuntu-natty-headless.img --arm=/home/coep/gem5 2/full_system_images/vmlinux.arm.smp.fb.3.2/vmlinux.arm.smp.fb.3.2"
and getting error as : "Usage: fs.py [options] fs.py: error: option --arm-iset: invalid choice: '/home/coep/gem5' (choose from 'arm', 'thumb', 'aarch64')"
please help me to solve this error.
Thank you.
I assume the --arm=/home/coep/gem5...vmlinux.arm.smp.fb.3.2 argument specifies the path to the guest kernel, in which case it should be --kernel=...:
build/ARM/gem5.opt \
configs/example/fs.py \
--disk-image=/home/coep/gem5\ 2/full_system_images/aarch32-ubuntu-natty-headless.img \
--kernel=/home/coep/gem5\ 2/full_system_images/vmlinux.arm.smp.fb.3.2/vmlinux.arm.smp.fb.3.2
Arguments and their explanations are found in configs/common/Options.py
There can be multiple reasons why are getting this error, One of them can be an incorrect path to the disk image files.
I have run the gem5 in the FS mode and have booted Linux on top of it on Ubuntu 18.04 LTS
You can follow the below steps, the first step is to download and install the full-system binary and disk image files.
1. $ mkdir full_system_image
2. $ cd full_system_image/
3. $ wget http://www.m5sim.org/dist/current/arm/aarch-system-2014-10.tar.bz2
4. $ tar jxf aarch-system-2014-10.tar.bz2
5. $ echo "export M5_PATH=/Path to the full_system_image directory/full_system_images/" >> ~/.bashrc
6. $ source ~/.bashrc
7. $ echo $M5_PATH (- check if the path is set correct)
Now the path has been set, the next step is to run the gem5 in FS mode.
1. connect to gem5 base directory
2. $ ./build/ARM/gem5.opt configs/example/fs.py --disk-image=/home/full_system_image/disks/aarch32-ubuntu-natty-headless.img
3. Note: --disk-image=path to the full_system_image/disks/aarch32-ubuntu-natty-headless.img
4. open a new terminal and listen to port 3456
5. $ telnet localhost 3456
6. Here 3456 is a port number on the gem5 terminal
7. this will take around 30 mins depending on the machine performance.
8. After this, at the end you will get something like this
input: AT Raw Set 2 keyboard as /devices/smb.14/motherboard.15/iofpga.17/1c060000.kmi/serio0/input/input0
input: touchkitPS/2 eGalax Touchscreen as
/devices/smb.14/motherboard.15/iofpga.17/1c070000.kmi/serio1/input/input2
kjournald starting. Commit interval 5 seconds
EXT3-fs (sda1): using internal journal
EXT3-fs (sda1): mounted filesystem with writeback data mode
VFS: Mounted root (ext3 filesystem) on device 8:1.
Freeing unused kernel memory: 292K (806aa000 - 806f3000)
random: init urandom read with 14 bits of entropy available
Ubuntu 11.04 gem5sim ttySA0
9. login as root
Voila, you have run the gem5 in FS mode.
note: backend error output: -v: -c: line 0: unexpected EOF while looking for matching `''
-v: -c: line 1: syntax error: unexpected end of file
ConEmuC: Root process was alive less than 10 sec, ExitCode=0.
Press Enter or Esc to close console...
This is error i am getting.
Also i have set the fish shell as default shell in WSL.
For WSL1 on windows 10 build later than 1909 (yes wsl2 is available to me but for corporate reasons i cant use it)
Try setting your command to wsl.exe -new_console:d:C:\_stuff\code -cur_console:p5 and the task parameters to /dir "c:/_stuff/code" /icon "c:/_distros/ubuntu/ubuntu1804.exe"
You may need to change the file locations to make the command and parameters suitable for your setup. c:/_stuff/code is where i keep all my repositories and c:/_distros/ubuntu is where i have installed ubuntu.
I have a simple rule to generate a file in Snakemake. Running snakemake results in an immediate error that it cannot find the generated file, even when --latency-wait is specified as a command line option.
However, this does seem to be a latency-related issue, as this Snakefile runs without problems on a local machine. The output below is on a system that has known latency problems.
Contents of Snakefile:
rule generate_file:
output:
"dummy.txt"
shell:
"head --bytes 1024 < /dev/zero | base64 > '{output}'; ls"
Commands:
$ snakemake --version
5.2.0
$ snakemake -p --latency-wait 10
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 generate_file
1
rule generate_file:
output: dummy.txt
jobid: 0
head --bytes 1024 < /dev/zero | base64 > 'dummy.txt'; ls
dummy.txt Snakefile
MissingOutputException in line 1 of /home/user/project/Snakefile:
[Errno 2] No such file or directory: ''
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
Removing output files of failed job generate_file since they might be corrupted:
dummy.txt
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/user/project/.snakemake/log/2018-08-08T101648.774072.snakemake.log
Interestingly, the ls command shows the file is created and visible.
Your rule creates output file dummy.txt when used with snakemake version 5.2.2 and linux, and snakemake ends successfully. Perhaps it is a bug in version 5.2.0? I don't see anything about it in change logs though.
On related note, use of head in shell command used to result in non-zero exit status error. Apparently recent version behaves differently in this respect.
I am combining Singularity & Snakemake to create a workflow for some sequencing data. I modeled my pipeline after this git project https://github.com/sci-f/snakemake.scif. The version of the pipeline that does not use Singularity runs absolutely fine. The version that uses Singularity always stops after the first rule with the following error:
$ singularity run --bind data/raw_data/:/scif/data/ /gpfs/data01/heinzlab/home/cag104/bin/chip-seq-pipeline/chip-seq-pipeline-hg38.simg run snakemake all
[snakemake] executing /bin/bash /scif/apps/snakemake/scif/runscript all
Copying Snakefile to /scif/data
Copying config.yaml to /scif/data
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 all
1 bowtie2_mapping
1 create_bigwig
1 create_tag_directories
1 fastp
1 fastqc
1 quality_metrics
1 samtools_index
8
rule fastp:
input: THP-1_PU1-cMyc_PU1_sc_S40_R1_001.fastq.gz
output: fastp/THP-1_PU1-cMyc_PU1_sc_S40_R1_001.fastp.fastq.gz, fastp_report/THP-1_PU1-cMyc_PU1_sc_S40_R1_001.html, fastp_report/THP-1_PU1-cMyc_PU1_sc_S40_R1_001.json
log: logs/fastp/THP-1_PU1-cMyc_PU1_sc_S40_R1_001.log
jobid: 7
wildcards: sample=THP-1_PU1-cMyc_PU1_sc_S40_R1_001
usage: scif run [-h] [cmd [cmd ...]]
positional arguments:
cmd app and optional arguments to target for the entry
optional arguments:
-h, --help show this help message and exit
Waiting at most 5 seconds for missing files.
MissingOutputException in line 16 of /scif/data/Snakefile:
Missing files after 5 seconds:
fastp/THP-1_PU1-cMyc_PU1_sc_S40_R1_001.fastp.fastq.gz
fastp_report/THP-1_PU1-cMyc_PU1_sc_S40_R1_001.html
fastp_report/THP-1_PU1-cMyc_PU1_sc_S40_R1_001.json
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
Will exit after finishing currently running jobs.
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /scif/data/.snakemake/log/2018-04-06T224320.958604.snakemake.log
The directory however does create the fastp and fastp_report directories as well as the logs directory. I tried increasing the latency to 50 seconds, but I still get the same error.
Any ideas on what to try here?