W-Hsu commented 3 years ago

Didn't encounter your problem. Can you upload a screenshot of your log file?

Tom111-lhx commented 3 years ago

ok ,is this dedisperse.log

------------------ 原始邮件 ------------------ 发件人: "anonymous"<notifications@github.com>; 发送时间: 2021年1月7日(星期四) 下午3:40 收件人: "W-Hsu/ASC21-preliminary"<ASC21-preliminary@noreply.github.com>; 抄送: "数学1李昊翕2019302998"<2388979406@qq.com>; "Author"<author@noreply.github.com>; 主题: Re: [W-Hsu/ASC21-preliminary] Hello ,have you run the correct result about python GBT pipeline.py,I have something in trouble about the chkfopen(),may be something wrong in prepsubband (#1)

Didn't encounter your problem. Can you upload a screenshot of your log file?

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Tom111-lhx commented 3 years ago

` 'Sband_DM17.75.sub16' 'Sband_DM17.75.sub17' 'Sband_DM17.75.sub18' 'Sband_DM17.75.sub19' 'Sband_DM17.75.sub20' 'Sband_DM17.75.sub21' 'Sband_DM17.75.sub22' 'Sband_DM17.75.sub23' 'Sband_DM17.75.sub24' 'Sband_DM17.75.sub25' 'Sband_DM17.75.sub26' 'Sband_DM17.75.sub27' 'Sband_DM17.75.sub28' 'Sband_DM17.75.sub29' 'Sband_DM17.75.sub30' 'Sband_DM17.75.sub31' numout=531000/n De-dispersing using: Subbands = 32 Average DM = 17.75

^MAmount complete = 0%^MAmount complete = 1%^MAmount complete = 2%^MAmount complete = 3%^MAmount complete = 4%^MAmount complete = 5%^MAmount complete = 6%^MAmount complete = 7%^MAmount complete = 8%^MAmount complete = 9%^MAmount complete = 10%^MAmount complete = 11%^MAmount complete = 12%^MAmount complete = 13%^MAmount complete = 14%^MAmount complete = 15%^MAmount complete = 16%^MAmount complete = 17%^MAmount complete = 18%^MAmount complete = 19%^MAmount complete = 20%^MAmount complete = 21%^MAmount complete = 22%^MAmount complete = 23%^MAmount complete = 24%^MAmount complete = 25%^MAmount complete = 26%^MAmount complete = 27%^MAmount complete = 28%^MAmount complete = 29%^MAmount complete = 30%^MAmount complete = 31%^MAmount complete = 32%^MAmount complete = 33%^MAmount complete = 34%^MAmount complete = 35%^MAmount complete = 36%^MAmount complete = 37%^MAmount complete = 38%^MAmount complete = 39%^MAmount complete = 40%^MAmount complete = 41%^MAmount complete = 42%^MAmount complete = 43%^MAmount complete = 44%^MAmount complete = 45%^MAmount complete = 46%^MAmount complete = 47%^MAmount complete = 48%^MAmount complete = 49%^MAmount complete = 50%^MAmount complete = 51%^MAmount complete = 52%^MAmount complete = 53%^MAmount complete = 54%^MAmount complete = 55%^MAmount complete = 56%^MAmount complete = 57%^MAmount complete = 58%^MAmount complete = 59%^MAmount complete = 60%^MAmount complete = 61%^MAmount complete = 62%^MAmount complete = 63%^MAmount complete = 64%^MAmount complete = 65%^MAmount complete = 66%^MAmount complete = 67%^MAmount complete = 68%^MAmount complete = 69%^MAmount complete = 70%^MAmount complete = 71%^MAmount complete = 72%^MAmount complete = 73%^MAmount complete = 74%^MAmount complete = 75%^MAmount complete = 76%^MAmount complete = 77%^MAmount complete = 78%^MAmount complete = 79%^MAmount complete = 80%^MAmount complete = 81%^MAmount complete = 82%^MAmount complete = 83%^MAmount complete = 84%^MAmount complete = 85%^MAmount complete = 86%^MAmount complete = 87%^MAmount complete = 88%^MAmount complete = 89%^MAmount complete = 90%^MAmount complete = 91%^MAmount complete = 92%^MAmount complete = 93%^MAmount complete = 94%^MAmount complete = 95%^MAmount complete = 96%^MAmount complete = 97%^MAmount complete = 98%

Done.`

Tom111-lhx commented 3 years ago

Done. Data points written: 525600

Error in chkfopen(): No such file or directory

W-Hsu commented 3 years ago

Can you run the whole routine correctly?

Tom111-lhx commented 3 years ago

Is it a presto version issue? no ,I stopped at ================sifting candidates================== Traceback (most recent call last): File "pipeline.py", line 293, in cands = ACCEL_sift(zmax) File "pipeline.py", line 251, in ACCELsift if len(re.findall("[0-9][0-9][0-9]M_" , inffiles[0])): and I read the pipeline.py,.May be there is something about prepsubband.c.

Tom111-lhx commented 3 years ago

I use the latest presto-master(presto3.0.1).

Tom111-lhx commented 3 years ago

I installed presto with fftw , tempo , cfisio , pgplot environments,and I do make makewisdom ;make prep ; make ;cd .. ; pip install ..I guess everything is OK,but I do python GBT... pipeline.py ,there are someting wrong .

W-Hsu commented 3 years ago

No, I'm using the latest version too. I just re-checked my dedisperse.log file, and I do find that I have the same problem... But I have the correct results at last. According to your error message if len(re.findall("[0-9][0-9][0-9]M" , inffiles[0])): I suggest you check if the files generate properly in subbands/ directory.

Tom111-lhx commented 3 years ago

in my dedisperse.log ,I just have .dat .fft ,but no .inf , and all my ".dat",".fft"file is empty.

Tom111-lhx commented 3 years ago

Must I install sigproc,and tempo2 or other things which are not in INSTALL guide.

W-Hsu commented 3 years ago

TEMPO is a must. btw. Are your environment variables set? Or are you using self-compile libraries or the apt/yum ones?

Tom111-lhx commented 3 years ago

I just see that in my subbands: -rw-rw-r-- 1 wangsijun wangsijun 29380 Jan 7 16:39 accelsearch.log -rw-rw-r-- 1 wangsijun wangsijun 43749 Jan 7 16:39 dedisperse.log -rw-rw-r-- 1 wangsijun wangsijun 11236 Jan 7 16:39 fft.log -rw-rw-r-- 1 wangsijun wangsijun 0 Jan 7 16:39 Sband_DM81.00.fft -rw-rw-r-- 1 wangsijun wangsijun 0 Jan 7 16:39 Sband_DM81.50.dat -rw-rw-r-- 1 wangsijun wangsijun 0 Jan 7 16:39 Sband_DM81.50.fft -rw-rw-r-- 1 wangsijun wangsijun 0 Jan 7 16:39 Sband_DM82.00.dat -rw-rw-r-- 1 wangsijun wangsijun 0 Jan 7 16:39 Sband_DM82.00.fft -rw-rw-r-- 1 wangsijun wangsijun 0 Jan 7 16:39 Sband_DM82.50.dat -rw-rw-r-- 1 wangsijun wangsijun 0 Jan 7 16:39 Sband_DM82.50.fft -rw-rw-r-- 1 wangsijun wangsijun 0 Jan 7 16:39 Sband_DM83.00.dat -rw-rw-r-- 1 wangsijun wangsijun 0 Jan 7 16:39 Sband_DM83.00.fft -rw-rw-r-- 1 wangsijun wangsijun 0 Jan 7 16:39 Sband_DM83.50.dat

Tom111-lhx commented 3 years ago

`#!/bin/bash PATH=$PATH:$HOME/bin:/home/wangsijun/project/task6/astrosoft/presto/bin:/home/wangsijun/project/task6/astrosoft/pgplot/bin:/home/wangsijun/project/task6/astrosoft/presto/bin:/nfshome/mcc/pfits:/home/wangsijun/project/task6/astrosoft/optimus:/home/wangsijun/project/task6/astrosoft/fv:/home/wangsijun/project/task6/astrosoft/psrcat_tar:/home/wangsijun/project/task6/astrosoft/tempo/src/ LD_LIBRARY_PATH=/home/wangsijun/project/task6/astrosoft/presto/lib:/home/wangsijun/project/task6/astrosoft/pgplot:/home/wangsijun/project/task6/astrosoft/fftw/lib:/home/wangsijun/project/task6/astrosoft/cfitsio/lib C_INCLUDE_PATH=/home/wangsijun/project/task6/astrosoft/presto/include:/home/wangsijun/project/task6/astrosoft/cfitsio/include PKG_CONFIG_PATH=/home/wangsijun/project/task6/astrosoft/cfitsio/lib/pkgconfig:/home/wangsijun/project/task6/astrosoft/fftw/lib/pkgconfig PYTHONPATH=/home/wangsijun/project/task6/astrosoft/presto/lib/python:/home/wangsijun/project/task6/astrosoft/presto/python PGPLOT_DIR=/home/wangsijun/project/task6/astrosoft/pgplot PGPLOT_FONT=/home/wangsijun/project/task6/astrosoft/pgplot/grfont.dat PGPLOT_DEV=/xwine PGPLOT_LIB="-L /usr/X11R6/lib -lX11 -L /home/wangsijun/project/task6/astrosoft/pgplot -lpgplot" PRESTO=/home/wangsijun/project/task6/astrosoft/presto TEMPO=/home/wangsijun/project/task6/astrosoft/tempo PSRCAT_FILE=/home/wangsijun/project/task6/astrosoft/psrcat_tar/psrcat.db

export PATH

export LD_LIBRARY_PATH

export C_INCLUDE_PATH

export PKG_CONFIG_PATH

export PYTHONPATH

export PGPLOT_DIR

export PGPLOT_FONT

export PGPLOT_DEV

export PGPLOT_LIB

export PRESTO

export TEMPO

export PSRCAT_FILE

ANACONDA=/home/wangsijun/project/apps/anaconda2 export PATH="$ANACONDA/bin:$PATH"`

Tom111-lhx commented 3 years ago

I set my library in /task6/sentenv1.sh

Tom111-lhx commented 3 years ago

I do it on cloud platform, not on my own computer.

W-Hsu commented 3 years ago

Try to use the pgplot5 installed with apt (if your os is debian/ubuntu) The self-compiled soft can cause trouble.

Tom111-lhx commented 3 years ago

but I am not the root user in the cloud platform, and in the cloud platform, my os is centos.

Tom111-lhx commented 3 years ago

my install step : download:ftp://ftp.astro.caltech.edu/pub/pgplot/pgplot5.2.tar.gz cd /home/m/Download wget ftp://ftp.astro.caltech.edu/pub/pgplot/pgplot5.2.tar.gz tar -zxvf pgplot5.2.tar.gz mkdir /home/m/astrosoft/pgplot cd /home/m/astrosoft/pgplot cp /home/m/Download/pgplot/drivers.list . vi drivers.list add:PS X-windows VPS、CPS,VCPS do:/home/m/astrosoft/new/pgplot/makemake /home/m/astrosoft/new/pgplot linux g77_gcc drivers.list grexec.f grpckg1.inc makefile pgplot.inc rgb.txt vi makefile FCOMPL=g77 >FCOMPL=gfortran sudo yum install libX11-devel make make cpg

W-Hsu commented 3 years ago

Hmm.. Seems to have no problem. I just noticed that something may be wrong with the second line's tail of your setenv1.sh PATH=$PATH:.../home/wangsijun/project/task6/astrosoft/tempo/src/, why not tempo/bin? Can you call the tempo command? btw. Don't run your setenv1.sh like ./setenv1.sh, use . setenv1.sh instead.

Tom111-lhx commented 3 years ago

so I should modify it ,should I remake in presto/src.

W-Hsu commented 3 years ago

Make it with a prefix. Like:

./configure --prefix=/home/wangsijun/project/task6/astrosoft/tempo/
make
make install

Tom111-lhx commented 3 years ago

in /presto/src ?

W-Hsu commented 3 years ago

No. If you can't find your tempo command, in tempo/bin, maybe you need to rebuild tempo. If the new tempo PATH is set, maybe you don't have to rebuild PRESTO.

Tom111-lhx commented 3 years ago

OK,I will try it

Tom111-lhx commented 3 years ago

what's your fftw version I use fftw-3.3.5

Tom111-lhx commented 3 years ago

Ummm,I still failed

Tom111-lhx commented 3 years ago

do you creat ".inf "file in your subbands?

Tom111-lhx commented 3 years ago

Maybe something wrong with PSRFITS，SIGPROC，I have not install it

W-Hsu commented 3 years ago

I use fftw3.3.8. It is really confusing. I cannot think of better solutions.

Tom111-lhx commented 3 years ago

can you give me some of your result and Path,I want find something different.

Tom111-lhx commented 3 years ago

and I want to know if there is .inf in your dedisperse.log. I feel crazy and tired about the presto .

W-Hsu commented 3 years ago

export PGPLOT_DIR=/usr/lib/pgplot5
export PRESTO=/home/whsu/opt/presto
export TEMPO=/home/whsu/opt/tempo
PATH=$PRESTO/bin:$PATH
PATH=$TEMPO/bin:$PATH
export PATH

These are all the environments that I set. There is no inf file mentioned in my dedisperse.log. However, the inf files are created during prepsubband.

Tom111-lhx commented 3 years ago

but where are your fftw or cfisio's path?

W-Hsu commented 3 years ago

I installed them with my package manager - rather than compile them all by myself. The pkg-config command invoked in $PRESTO/src/Makefile will handle it automatically.

Tom111-lhx commented 3 years ago

can i do The pkg-config command on centos?

W-Hsu commented 3 years ago

It shall be universal. But it needs *.ps files as its guide... The configuration is rather complex. Are you preparing for the ASC competition? Maybe you should consult your teacher. If you can get access to root permission, you can have a try on your package manager.

Tom111-lhx commented 3 years ago

He said that maybe there are something wrong about the pipeline.py. because He thought my enxironment is right.

Tom111-lhx commented 3 years ago

I rebuild the presto ,and do the command: File "/home/wangsijun/project/task5/astrosoft/presto/python/presto/sifting.py", line 13, in from presto.presto import candidate_sigma ImportError: No module named presto

W-Hsu commented 3 years ago

Yeah, you are very close to success. Simply delete the parameter will work.

Tom111-lhx commented 3 years ago

where is parameter

W-Hsu commented 3 years ago

I thought of my own problem...never mind So which line of pipeline.py raised this?

Tom111-lhx commented 3 years ago

sorry,I didn't understand,shall I need to delete the line in sifting.py or in pipeline.py

Tom111-lhx commented 3 years ago

File "pipeline.py", line 9, in from presto import sifting File "/home/wangsijun/project/task5/astrosoft/presto/python/presto/sifting.py", line 13, in from presto.presto import candidate_sigma ImportError: No module named presto

Tom111-lhx commented 3 years ago

at the beginning, I modifed the line 9 which is "import sifting " to "from presto import sifting", and then the error appeared

W-Hsu commented 3 years ago

Can you import presto.presto in the interactive python?

Tom111-lhx commented 3 years ago

I do pip install .

Tom111-lhx commented 3 years ago

it is in /project/wangsijun/apps/anaconda2/lib/python2.7/site-packages

W-Hsu commented 3 years ago

You can try uninstall it first and install it... It may work.

Tom111-lhx commented 3 years ago

I find that there is two presto, one is in presto/python/presto, the other is /home/wangsijun/project/apps/anaconda2/lib/python2.7/site-packages/presto/presto do you think it is right,all the presto have sifting.py

W-Hsu / ASC21-preliminary

Hello ,have you run the correct result about python GBT pipeline.py,I have something in trouble about the chkfopen(),may be something wrong in prepsubband #1

export PATH

export C_INCLUDE_PATH

export PKG_CONFIG_PATH

export PYTHONPATH

export PGPLOT_FONT

export PGPLOT_DEV

export PGPLOT_LIB

export TEMPO

export PSRCAT_FILE