Cptcore Error

[Benjamin Kwenda]

Greetings to you all. I had to do a fresh installation of PyCPT on my laptop. After doing everything I then tried to run the jupyter notebook. I am getting the error that is attached here.

Makefile:6: make.inc: No such file or directory
make[1]: *** No rule to make target 'make.inc'.  Stop. 

make: *** [Makefile:87: lapack/lapack/liblapack.a] Error 2 

Regards

--

Benjamin M Kwenda

Agriculture Meteorologist

Long Range Forecasting

Meteorological Services Department

Belvedere, Harare

(+263) 773504696

Skype: bkwenda_1

Scientists of today think deeply instead of clearly. One must be sane to think clearly, but one can think deeply and be quite insane!!!!- Nikola Tesla

[Tamirat Bekele]

Hi Benjamin,

Please be a little bit verbose.

best,

On Tue, 29 Nov 2022, 15:43 Benjamin Kwenda, <bkw...@gmail.com> wrote:

Greetings to you all. I had to do a fresh installation of PyCPT on my laptop. After doing everything I then tried to run the jupyter notebook. I am getting the error that is attached here.

Makefile:6: make.inc: No such file or directory
make[1]: *** No rule to make target 'make.inc'.  Stop. 

make: *** [Makefile:87: lapack/lapack/liblapack.a] Error 2 

Regards

--

Benjamin M Kwenda

Agriculture Meteorologist

Long Range Forecasting

Meteorological Services Department

Belvedere, Harare

(+263) 773504696

Skype: bkwenda_1

Scientists of today think deeply instead of clearly. One must be sane to think clearly, but one can think deeply and be quite insane!!!!- Nikola Tesla

--

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[Benjamin Kwenda]

Dear Tamirat

So this is what happened. I had to do a reinstallation of Ubuntu on my Windows laptop. After that, I installed all the other packages such as build essential, cartopy, matplotlib, nbconvert etc using the commands in the Powerpoint Presentation. Afterwards, I then started running the script in the Jupyter Notebook. On running the first cell where there is the following lines

1. import cptdl as dl
2. import cptio as cio
3. import cptcore as cc
4. import cptextras as ce

Now when it gets to line 3, I am getting the error that I mentioned. 

Makefile:6: make.inc: No such file or directory
make[1]: *** No rule to make target 'make.inc'.  Stop.
make: *** [Makefile:87: lapack/lapack/liblapack.a] Error 2

File ~/anaconda3/envs/pycpt_environment/lib/python3.10/site-packages/cptcore-1.0.10-py3.9.egg/cptcore/__init__.py:22
     20 import platform
     21 if platform.system() == 'Linux':
---> 22     install_cpt_linux()
     24 CPT_CITATION = "Simon J. Mason, Michael K. Tippet, Lulin Song, Ángel G. Muñoz. 2021. Climate Predictability Tool version 17.5.2. Columbia University Academic Commons. https://doi.org/10.7916/d8-em2t-k781"
     25 PYCPTV1_CITATION = "Muñoz, Á.G., Robertson, A.W., Turkington, T., Mason, S.J., and contributors, 2019: 'PyCPT: a Python interface and enhancement for IRI's Climate Predictability Tool'."

File ~/anaconda3/envs/pycpt_environment/lib/python3.10/site-packages/cptcore-1.0.10-py3.9.egg/cptcore/utilities.py:323, in install_cpt_linux()
    321 subprocess.call(['make'], cwd=str((path/'fortran'/'Linux'/'CPT'/'17.7.4').absolute()))
    322 CPT_EXECUTABLE = (path / 'fortran' / 'Linux' / 'CPT' / '17.7.4').absolute() / 'CPT.x'
--> 323 assert CPT_EXECUTABLE.is_file(), 'FAILED TO COMPILE CPT'
    324 return CPT_EXECUTABLE
 

AssertionError: FAILED TO COMPILE CPT 

 

[Bohar Singh]

Hi Benjamin, 

It’s lapack library bug. 

To solve this problem 

Manually go to CPT directory and then 

cd lapack/lapack

mv make.inc.example make.inc

Now run cell 1 again 

Let us know if it works

Regards

Bohar

On Nov 29, 2022, at 9:07 AM, Benjamin Kwenda <bkw...@gmail.com> wrote:

Dear Tamirat

So this is what happened. I had to do a reinstallation of Ubuntu on my Windows laptop. After that, I installed all the other packages such as build essential, cartopy, matplotlib, nbconvert etc using the commands in the Powerpoint Presentation. Afterwards, I then started running the script in the Jupyter Notebook. On running the first cell where there is the following lines

1. import cptdl as dl
2. import cptio as cio
3. import cptcore as cc
4. import cptextras as ce

Now when it gets to line 3, I am getting the error that I mentioned. 

Makefile:6: make.inc: No such file or directory
make[1]: *** No rule to make target 'make.inc'.  Stop.
make: *** [Makefile:87: lapack/lapack/liblapack.a] Error 2

File ~/anaconda3/envs/pycpt_environment/lib/python3.10/site-packages/cptcore-1.0.10-py3.9.egg/cptcore/__init__.py:22
     20 import platform
     21 if platform.system() == 'Linux':
---> 22     install_cpt_linux()
     24 CPT_CITATION = "Simon J. Mason, Michael K. Tippet, Lulin Song, Ángel G. Muñoz. 2021. Climate Predictability Tool version 17.5.2. Columbia University Academic Commons. https://doi.org/10.7916/d8-em2t-k781"
     25 PYCPTV1_CITATION = "Muñoz, Á.G., Robertson, A.W., Turkington, T., Mason, S.J., and contributors, 2019: 'PyCPT: a Python interface and enhancement for IRI's Climate Predictability Tool'."

File ~/anaconda3/envs/pycpt_environment/lib/python3.10/site-packages/cptcore-1.0.10-py3.9.egg/cptcore/utilities.py:323, in install_cpt_linux()
    321 subprocess.call(['make'], cwd=str((path/'fortran'/'Linux'/'CPT'/'17.7.4').absolute()))
    322 CPT_EXECUTABLE = (path / 'fortran' / 'Linux' / 'CPT' / '17.7.4').absolute() / 'CPT.x'
--> 323 assert CPT_EXECUTABLE.is_file(), 'FAILED TO COMPILE CPT'
    324 return CPT_EXECUTABLE
 

AssertionError: FAILED TO COMPILE CPT 

  
<image.png>

On Tue, Nov 29, 2022 at 3:29 PM Tamirat Bekele <atomic...@gmail.com> wrote:

Hi Benjamin,

Please be a little bit verbose.

best,

On Tue, 29 Nov 2022, 15:43 Benjamin Kwenda, <bkw...@gmail.com> wrote:

Greetings to you all. I had to do a fresh installation of PyCPT on my laptop. After doing everything I then tried to run the jupyter notebook. I am getting the error that is attached here.

Makefile:6: make.inc: No such file or directory
make[1]: *** No rule to make target 'make.inc'.  Stop. 

make: *** [Makefile:87: lapack/lapack/liblapack.a] Error 2 

Regards

<image.png>

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["Ángel G. Muñoz"]

Hi,

Bohar, you need to recompile after making that change in lapack, right?

Ángel

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[Bohar Singh]

Thanks for correction Ángel, I miss that step. 

Hi Keenness, 

Go to this directory 

..../pycpt_environment\lib\python3.9\site-packages\cptcore-1.0.8-py3.8\cptcore\fortran\Linux\CPT\17.7.4\lapack\lapack

Change file name  make.inc.example to make.inc

mv make.inc.example make.inc

then come back to directory 17.7.4 by 

Cd ../.. 

And recompile 

make

On Nov 29, 2022, at 9:40 AM, KEENNESS MANG'ANDA <pke...@gmail.com> wrote:

Here is the path, I managed to find it 

..../pycpt_environment\lib\python3.9\site-packages\cptcore-1.0.8-py3.8\cptcore\fortran\Linux\CPT\17.7.4\lapack\lapack

Regards

Keenness Mang'anda

Principal Meteorologist

Department of climate change and Meteorological  services

P.O. Box 1808

Blantyre

Phone: (+265) 993 042 180

'''''''''''''''''''The Lord is my shepherd, I shall not want''''''''''''''''''''''''''''''''

On Tue, 29 Nov 2022 at 16:33, KEENNESS MANG'ANDA <pke...@gmail.com> wrote:

Can you elaborate on the CPT directory, Which directory is this?

Regards

Keenness Mang'anda

Principal Meteorologist

Department of climate change and Meteorological  services

P.O. Box 1808

Blantyre

Phone: (+265) 993 042 180

'''''''''''''''''''The Lord is my shepherd, I shall not want''''''''''''''''''''''''''''''''

To view this discussion on the web visit https://groups.google.com/a/iri.columbia.edu/d/msgid/pycpt-esa/9407519B-99C7-434F-BEAC-BAEB388D2DE6%40iri.columbia.edu.

For more options, visit https://groups.google.com/a/iri.columbia.edu/d/optout.

Best Regards

Bohar Singh Ph.D.

Associate Research Scientist
International Research Institute for Climate and Society 
The Earth Institute at Columbia University 
61 Route 9W Monell Building 
Palisades, NY 10964-8000 

[KEENNESS MANG'ANDA]

Can you elaborate on the CPT directory, Which directory is this?

Regards

Keenness Mang'anda

Principal Meteorologist

Department of climate change and Meteorological  services

P.O. Box 1808

Blantyre

Phone: (+265) 993 042 180

'''''''''''''''''''The Lord is my shepherd, I shall not want''''''''''''''''''''''''''''''''

On Tue, 29 Nov 2022 at 16:18, Bohar Singh <bo...@iri.columbia.edu> wrote:

To view this discussion on the web visit https://groups.google.com/a/iri.columbia.edu/d/msgid/pycpt-esa/9407519B-99C7-434F-BEAC-BAEB388D2DE6%40iri.columbia.edu.

[KEENNESS MANG'ANDA]

Here is the path, I managed to find it 

..../pycpt_environment\lib\python3.9\site-packages\cptcore-1.0.8-py3.8\cptcore\fortran\Linux\CPT\17.7.4\lapack\lapack

Regards

Keenness Mang'anda

Principal Meteorologist

Department of climate change and Meteorological  services

P.O. Box 1808

Blantyre

Phone: (+265) 993 042 180

'''''''''''''''''''The Lord is my shepherd, I shall not want''''''''''''''''''''''''''''''''

On Tue, 29 Nov 2022 at 16:33, KEENNESS MANG'ANDA <pke...@gmail.com> wrote:

[Benjamin Kwenda]

Dear Bohar

Thanks for that but unfortunately after sorting out that error I am now getting a different one again. It seems as if it's a CPT error again.

PermissionError                           Traceback (most recent call last)
Cell In [3], line 2
      1 # Uncomment the following line & change the config filepath to save this configuration: 
----> 2 config_file = ce.save_configuration('test1.config', download_args, cpt_args, MOS, predictor_names, predictand_name )
      4 # Uncomment the following line & change the config filepath to load an existing configuration: 
      5 MOS, download_args, cpt_args, predictor_names, predictand_name = ce.load_configuration('test1.config')

File ~/anaconda3/envs/pycpt_environment/lib/python3.10/site-packages/cptextras-1.0.3-py3.9.egg/cptextras/configuration.py:87, in save_configuration(fname, download_args2, cpt_args2, MOS, predictors, predictand)
     83 tosave['cptcore_version'] = cc.__version__
     84 tosave['cptextras_version'] = __version__
---> 87 with open(fname, 'w') as f: 
     88     json.dump(tosave, f, indent=4, sort_keys=True)
     90 return fname

PermissionError: [Errno 13] Permission denied: 'test1.config'

Regards

[Andrew Robertson]

Hi Benjamin & all,

I’ve seen these "Permission denied” errors before when writing files to disk in PyCPT. I don’t know why they happen but try deleting 'test1.config’ if it already exists, then try running again. Perhaps someone else can clarify? Tamirat, have you seen this?

Best,

Andrew

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["Ángel G. Muñoz"]

Hi,

This happens sometimes with Python (not only PyCPT), yes. That function should check first if the file exists, and if so, delete it before writing the new file. I concur: manually deleting the file, or changing its name in the notebook, should solve the issue.

Ángel

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[Andrew Robertson]

Thanks Angel!

[Tamirat Bekele]

> >>> <mailto:pke...@gmail.com>> wrote:

> >>>

> >>> Here is the path, I managed to find it

> >>> ..../pycpt_environment\lib\python3.9\site-packages\cptcore-1.0.8-py3.8\c

> >>> ptcore\fortran\Linux\CPT\17.7.4\lapack\lapack

> >>>

> >>> Regards

> >>> Keenness Mang'anda

> >>> Principal Meteorologist

> >>>

> >>> Department of climate change and Meteorological  services

> >>> P.O. Box 1808

> >>> Blantyre

> >>> Phone: (+265) 993 042 180

> >>> '''''''''''''''''''The Lord is my shepherd, I shall not

> >>> want''''''''''''''''''''''''''''''''>>>

> >>> On Tue, 29 Nov 2022 at 16:33, KEENNESS MANG'ANDA <pke...@gmail.com <mailto:pke...@gmail.com>> wrote:

> >>>> Can you elaborate on the CPT directory, Which directory is this?

> >>>>

> >>>> Regards

> >>>> Keenness Mang'anda

> >>>> Principal Meteorologist

> >>>>

> >>>> Department of climate change and Meteorological  services

> >>>> P.O. Box 1808

> >>>> Blantyre

> >>>> Phone: (+265) 993 042 180

> >>>> '''''''''''''''''''The Lord is my shepherd, I shall not

> >>>> want''''''''''''''''''''''''''''''''>>>>

> >>>> On Tue, 29 Nov 2022 at 16:18, Bohar Singh <bo...@iri.columbia.edu <mailto:bo...@iri.columbia.edu>> wrote:

> >>>>> Hi Benjamin,

> >>>>>

> >>>>> It’s lapack library bug.

> >>>>> To solve this problem

> >>>>> Manually go to CPT directory and then

> >>>>> cd lapack/lapack

> >>>>> mv make.inc.example make.inc

> >>>>>

> >>>>> Now run cell 1 again

> >>>>>

> >>>>> Let us know if it works

> >>>>>

> >>>>> Regards

> >>>>> Bohar

> >>>>>

> >>>>>> On Nov 29, 2022, at 9:07 AM, Benjamin Kwenda <bkw...@gmail.com

> >>>>>>> <mailto:bkw...@gmail.com>> wrote: Greetings to you all. I had to

> >>>>>>> do a fresh installation of PyCPT on my laptop. After doing

> >>>>>>> everything I then tried to run the jupyter notebook. I am getting

> >>>>>>> the error that is attached here.

> >>>>>>>

> >>>>>>> Makefile:6: make.inc: No such file or directory

> >>>>>>> make[1]: *** No rule to make target 'make.inc'.  Stop.

> >>>>>>> make: *** [Makefile:87: lapack/lapack/liblapack.a] Error 2

> >>>>>>>

> >>>>>>> Regards

> >>>>>>> <image.png>

> >>>>>>>

> >>>>>>> --

> >>>>>>> Benjamin M Kwenda

> >>>>>>> Agriculture Meteorologist

> >>>>>>> Long Range Forecasting

> >>>>>>> Meteorological Services Department

> >>>>>>> Belvedere, Harare

> >>>>>>> (+263) 773504696

> >>>>>>> Skype: bkwenda_1

> >>>>>>>

> >>>>>>> Scientists of today think deeply instead of clearly. One must be

> >>>>>>> sane to think clearly, but one can think deeply and be quite

> >>>>>>> insane!!!!- Nikola Tesla

> >>>>>>>

> >>>>>>> --

> >>>>>>> You received this message because you are subscribed to the Google

> >>>>>>> Groups "pycpt-esa" group. To unsubscribe from this group and stop

> >>>>>>> receiving emails from it, send an email to

> >>>>>>> pycpt-esa+...@iri.columbia.edu

> >>>>>>> <mailto:pycpt-esa+...@iri.columbia.edu>. To view this

> >>>>>>> discussion on the web visit

> >>>>>>> https://groups.google.com/a/iri.columbia.edu/d/msgid/pycpt-esa/CAEE

> >>>>>>> VC%2BjH6aLfXvV3ycBqcqTSw1feXOCDrq%2Bz%3DZRnCqQzNtGcYQ%40mail.gmail.c

> >>>>>>> om

> >>>>>>> <https://groups.google.com/a/iri.columbia.edu/d/msgid/pycpt-esa/CAE

> >>>>>>> EVC%2BjH6aLfXvV3ycBqcqTSw1feXOCDrq%2Bz%3DZRnCqQzNtGcYQ%40mail.gmail.

> >>>>>>> com?utm_medium=email&utm_source=footer>. For more options, visit

> >>>>>>> https://groups.google.com/a/iri.columbia.edu/d/optout.>>

> >> Best Regards

> >> Bohar Singh Ph.D.

> >> Associate Research Scientist

> >> International Research Institute for Climate and Society

> >> The Earth Institute at Columbia University

> >> 61 Route 9W Monell Building

> >> Palisades, NY 10964-8000

Hi Andrew,

Yes, I often facing this issue too. As Angel mentioned, the existence of a file should be checked and either deleted, renamed, or forcefully overwritten.

regards,

--

Tamirat Bekele

Addis Ababa University

Cell: +251911152860

skype: tamirat.bekele

[Andrew Robertson]

Thanks Tamirat. I wonder why that is. Since this seems to be a general Python issue, have you found anything on this topic by googling it?

> Hi Andrew,
>
> Yes, I often facing this issue too. As Angel mentioned, the existence of a file should be checked and either deleted, renamed, or forcefully overwritten.
>
> regards,

[Tamirat Bekele]

Hi Andrew,

After reading your email, I have conducted some experiments with the python read/write function (i.e., open()) and my operating system (Linux) and understood that the "permission denied" message comes from the operating system (OS). The OS handle file permissions according to its default or user-specified "mask" configuration. These masks could be different for different directories. The problem happens when we try to cut/paste files from folder to folder or from one computer to another, having various "mask" configurations. The moved files inherit the destination system mask configuration. Therefore, the easy thing is to remove the old "test.config" file and let python script create a new one with the working directory default 'mask' configuration. I hope this explains it.

regards,

[Andrew Robertson]

Many thanks Tamirat. It’s very valuable to have this insight.

Best, Andy

[Maureen Ahiataku]

Dear Team,

I trust we are all doing well.

Thank you all for your input on resolving the cptcore error. 

I have followed the steps and changed the make.inc.example to make.inc

However, when I recompile "make" at .../17.7.4/, I get an error stating that the make file does not exist.

I attempted but failed to install it.

Please, I need help.

Thank you.

Maureen

[Andrew Robertson]

Thanks Maureen for your query. Please use pycpt...@iri.columbia.edu in the future, who’ll be able to get back to you.  The DJF issue has now been solved.

Best, Andy

[Maureen Ahiataku]

Hello Andrew,

Good to hear from you and many thanks for the feedback.

I will use the pycpt-help platform.

Best wishes,
Maureen

--

Maureen A. Ahiataku 

MSc. Atm. Science and Engineering

Ghana Meteorological Agency (GMet).

Dept. of Research and Applied Meteorology.

Hydrometeorology Unit.

Senior Meteorologist

Email: maureen...@gmail.com,

           m.ahi...@meteo.gov.gh

"Weather is life"

[KEENNESS MANG'ANDA]

I am experiencing this same error after a new installation, Please help me where I can find this tes.config file

Regards

Keenness Mang'anda

Principal Meteorologist

Department of climate change and Meteorological  services

P.O. Box 1808

Blantyre

Phone: (+265) 993 042 180

'''''''''''''''''''The Lord is my shepherd, I shall not want''''''''''''''''''''''''''''''''

To unsubscribe from this group and stop receiving emails from it, send an email to pycpt-esa+...@iri.columbia.edu.
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[Andrew Robertson]

Hi Keenness,

Thanks for reaching out!  I’ve copied pycpt...@iri.columbia.edu who will be able to help you.

Best,

Andy

[Aaron Kaplan]

Hello Keenness, Maureen, Tamirat, and everyone else who has reported problems compiling CPT.

Please delete your old conda environments and create a brand new one following the instructions at https://iri-pycpt.github.io/installation/ . Do not simply update a pre-existing environment, as that seems to be less predictable.

We have published a new version of PyCPT that includes a pre-compiled CPT executable. With the new version, it is impossible to get the compilation error that was reported on this thread, because there is nothing to compile. If you are still having problems after recreating your conda environment and installing the latest version, then I can think of two possible explanations:

1. conda is not installing the latest version for some reason, or
2. the error you're getting now is actually a different one from the one Maureen originally reported.

If reinstalling from scratch doesn't fix the problem, then please send the full text of the error message so that we can get to the bottom of this.

Thanks

-Aaron

[KEENNESS MANG'ANDA]

Thank you for the guild, I managed to install successfully.  I would like to know how we can incorporate ENACTS Data (local Data) into Pycpt instead of using CHIRPS data. Where can I add the path to ENACTS data?

Regards

Keenness Mang'anda

Principal Meteorologist

Department of climate change and Meteorological  services

P.O. Box 1808

Blantyre

Phone: (+265) 993 042 180

'''''''''''''''''''The Lord is my shepherd, I shall not want''''''''''''''''''''''''''''''''

[Aaron Kaplan]

 I would like to know how we can incorporate ENACTS Data (local Data) into Pycpt instead of using CHIRPS data. Where can I add the path to ENACTS data?

We don't currently have an easy answer to that question, but it's something we're actively working on. I hope to have an update within a week or two.

-Aaron 

[KEENNESS MANG'ANDA]

Thanks and looking forward to it