install error ubuntu #1529
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I am facing an install issue on ubuntu pc, below error message from make.log usr/bin/g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/basic/vx_cal -I../../../src/basic/vx_config -I../../../src/basic/vx_log -I../../../src/basic/vx_math -I../../../src/basic/vx_util -I../../../src/libcode/vx_afm -I../../../src/libcode/vx_analysis_util -I../../../src/libcode/vx_color -I../../../src/libcode/vx_data2d -I../../../src/libcode/vx_data2d_factory -I../../../src/libcode/vx_data2d_grib -I../../../src/libcode/vx_data2d_grib2 -I../../../src/libcode/vx_data2d_nccf -I../../../src/libcode/vx_data2d_nc_met -I../../../src/libcode/vx_data2d_nc_pinterp -I../../../src/libcode/vx_data2d_python -I../../../src/libcode/vx_python3_utils -I../../../src/libcode/vx_geodesy -I../../../src/libcode/vx_gis -I../../../src/libcode/vx_gnomon -I../../../src/libcode/vx_grid -I../../../src/libcode/vx_gsl_prob -I../../../src/libcode/vx_nav -I../../../src/libcode/vx_nc_obs -I../../../src/libcode/vx_nc_util -I../../../src/libcode/vx_pb_util -I../../../src/libcode/vx_plot_util -I../../../src/libcode/vx_pointdata_python -I../../../src/libcode/vx_ps -I../../../src/libcode/vx_pxm -I../../../src/libcode/vx_render -I../../../src/libcode/vx_regrid -I../../../src/libcode/vx_shapedata -I../../../src/libcode/vx_solar -I../../../src/libcode/vx_statistics -I../../../src/libcode/vx_stat_out -I../../../src/libcode/vx_bool_calc -I../../../src/libcode/vx_summary -I../../../src/libcode/vx_time_series -I../../../src/libcode/vx_series_data -I../../../src/libcode/vx_tc_util -I/home/sarr/MET101/external_libs/include -fopenmp -I/home/sarr/MET101/external_libs/include -I/home/sarr/MET101/external_libs/include -I/home/sarr/MET101/external_libs/include -I../../basic/vx_log -I../../basic/vx_util -I/usr/include/python3.8 -I/home/sarr/MET101/external_libs/include -DBLOCK4 -DWITH_GRIB2 -DWITH_PYTHON -DMET_BASE=""/home/sarr/MET101/share/met"" -MT libvx_util_a-data_cube.o -MD -MP -MF .deps/libvx_util_a-data_cube.Tpo -c -o libvx_util_a-data_cube.o Hope to solve this to follow the Metplus training. Thank you |
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Replies: 20 comments 20 replies
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Yep, I'm getting this too. Came here to post this, and found your issue. I'm guessing Intel doesn't complain about it. I'm using GCC 9.3.0. Edit: Looking a little more closely shape is defined as |
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On which file should I look at this? Thanks |
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data_plane_util.cc |
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something strange on my side because when I change the file I still get the
same error. When I open it again the file is again as before the change.
Look very strange
…On Sat, Mar 19, 2022 at 2:58 PM Kyle Gerheiser ***@***.***> wrote:
data_plane_util.cc
--- a/src/basic/vx_util/data_plane_util.cc 2022-03-18 22:29:42.000000000 -0400
+++ b/src/basic/vx_util/data_plane_util.cc 2022-03-18 22:30:44.000000000 -0400
@@ -253,7 +253,7 @@
#pragma omp parallel default(none) \
shared(mlog, dp, frac_dp, width, wrap_lon, t) \
- shared(use_climo, cmn, csd, vld_t, bad) \
+ shared(use_climo, cmn, csd, vld_t, bad, shape) \
private(x, y, n_vld, n_thr, gp, v)
{
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maybe a write permission, I am changing it and will try again
On Sat, Mar 19, 2022 at 5:40 PM Abdoulaye Sarr ***@***.***>
wrote:
… something strange on my side because when I change the file I still get
the same error. When I open it again the file is again as before the change.
Look very strange
On Sat, Mar 19, 2022 at 2:58 PM Kyle Gerheiser ***@***.***>
wrote:
> data_plane_util.cc
>
> --- a/src/basic/vx_util/data_plane_util.cc 2022-03-18 22:29:42.000000000 -0400
> +++ b/src/basic/vx_util/data_plane_util.cc 2022-03-18 22:30:44.000000000 -0400
> @@ -253,7 +253,7 @@
>
> #pragma omp parallel default(none) \
> shared(mlog, dp, frac_dp, width, wrap_lon, t) \
> - shared(use_climo, cmn, csd, vld_t, bad) \
> + shared(use_climo, cmn, csd, vld_t, bad, shape) \
> private(x, y, n_vld, n_thr, gp, v)
> {
>
> —
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I have problems with the file, when changed after compiling I have the same
error message, and when I open it appears without the change!
confusing for me
On Sat, Mar 19, 2022 at 5:57 PM Abdoulaye Sarr ***@***.***>
wrote:
… maybe a write permission, I am changing it and will try again
On Sat, Mar 19, 2022 at 5:40 PM Abdoulaye Sarr ***@***.***>
wrote:
> something strange on my side because when I change the file I still get
> the same error. When I open it again the file is again as before the change.
> Look very strange
>
> On Sat, Mar 19, 2022 at 2:58 PM Kyle Gerheiser ***@***.***>
> wrote:
>
>> data_plane_util.cc
>>
>> --- a/src/basic/vx_util/data_plane_util.cc 2022-03-18 22:29:42.000000000 -0400
>> +++ b/src/basic/vx_util/data_plane_util.cc 2022-03-18 22:30:44.000000000 -0400
>> @@ -253,7 +253,7 @@
>>
>> #pragma omp parallel default(none) \
>> shared(mlog, dp, frac_dp, width, wrap_lon, t) \
>> - shared(use_climo, cmn, csd, vld_t, bad) \
>> + shared(use_climo, cmn, csd, vld_t, bad, shape) \
>> private(x, y, n_vld, n_thr, gp, v)
>> {
>>
>> —
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>> <dtcenter/METplus#1528>,
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That's an issue with your system, permissions, or editor. I was able to compile with the given change. |
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Hello, And thank you for your question. I converted your initial Github issue to a Discussions, as Discussions is a better place to gather METplus community input and asking general questions to resolve problems with a feature of METplus. If a Discussions topic reveals the need to update or fix code within the system, we can then create Github issues to address them. From the above conversation, it seems like the solution may be within a permissions setting (thank you @kgerheiser for stepping through the install error!). Can you confirm what the solution was, if there has been one? If not, we can assign one of our team to look into this and try to help you find a solution. |
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@j-opatz the See this patch: |
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Hi @kgerheiser, thank you for discovering this, bringing it to our attention, and finding a solution. As far as I am aware our team has not tried compiling MET using GCC 9. The code is developed and tested using GCC 8.3.0. We will create a GitHub issue to make this fix and make sure that it does not break any functionality. I will post a link to the issue here once it has been created. |
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As @georgemccabe mentioned, we'll be working on this fix and getting it integrated into MET. You can now follow the issue to track its progress. |
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I followed this many times but on my system whenever I make the change and compile there is something strange that automatically |
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Hi @fipoucat, what is likely happening is the compilation script (compile_MET_all.sh) is wiping out the directory that contains the MET source code and extracting the tar file automatically. If you have already run the script and the MET source code is in place, then you should be able to make the change that you are trying to make, then set the USE_MET_TAR_FILE environment variable to a string that is anything but "TRUE" and rerun the compilation script. If using bash: If using csh: This should skip the step of replacing the source code from the tar file and allow you to build with the change you made. Please let me know if this does not work and I can take a closer look. |
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@george this has fixed the above-mentioned issue, now during the
compilation, there are other errors related to python with undefined
references.
I"ll check it before posting the error.
…On Wed, Mar 23, 2022 at 6:32 PM George McCabe ***@***.***> wrote:
Hi @fipoucat <https://github.com/fipoucat>, what is likely happening is
the compilation script (compile_MET_all.sh) is wiping out the directory
that contains the MET source code and extracting the tar file
automatically. If you have already run the script and the MET source code
is in place, then you should be able to make the change that you are trying
to make, then set the USE_MET_TAR_FILE environment variable to a string
that is anything but "TRUE" and rerun the compilation script.
If using bash:
export USE_MET_TAR_FILE=FALSE
If using csh:
setenv USE_MET_TAR_FILE FALSE
This should skip the step of replacing the source code from the tar file
and allow you to build with the change you made. Please let me know if this
does not work and I can take a closer look.
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@fipoucat , I am sorry you are continuing to run into errors. To my knowledge GCC 8.3.0 is the highest version of the compiler that we have used to build MET internally. If you continue to run into issues, I would recommend using this version of the compiler if you are able. The next METplus training session on March 29 will be focused on running METplus on AWS, so you will not need to have MET installed locally to follow along with the content. If you do not have access to the METplus AMI and would like to gain access, please send me your email address so I can send it to the team member who sets them up. |
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@georgemccabe regarding the version of gcc, in my case it's more related to python because I can compile with success when I remove --enable-python. Is there any specific version of python required because I tried with 3.8 and 3.9 or maybe something wrong with python LD and INC configs |
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If it compiles (doesn't fail with not finding |
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I know MET has been built using Python 3.8. We typically advice users to use the python3-config command to generate the values to set for MET_PYTHON_LD and MET_PYTHON_CC. If using bash:
These values may need to be slightly modified depending on what is output, but it is a good start. Just make sure that the python3-config command corresponds to the same version of python3 that you want to use for the build. |
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I was still working on my issue but still have errors, I'll stop here for
the moment, below the typical error messages I am having:
python_dataplane.cc:(.text+0x2ce): undefined reference to `PyErr_Occurred'
/usr/bin/ld: python_dataplane.cc:(.text+0x2dd): undefined reference to
`PyErr_Print'
/usr/bin/ld: python_dataplane.cc:(.text+0x3f9): undefined reference to
`PySys_SetArgv'
/usr/bin/ld: python_dataplane.cc:(.text+0x410): undefined reference to
`PyImport_ImportModule'
/usr/bin/ld: python_dataplane.cc:(.text+0x42f): undefined reference to
`PyImport_ReloadModule'
/usr/bin/ld: python_dataplane.cc:(.text+0x43b): undefined reference to
`PyErr_Occurred'
/usr/bin/ld: python_dataplane.cc:(.text+0x44e): undefined reference to
`PyErr_Print'
/usr/bin/ld: python_dataplane.cc:(.text+0x579): undefined reference to
`PyModule_GetDict'
/usr/bin/ld: python_dataplane.cc:(.text+0x5a4): undefined reference to
`PyUnicode_FromString'
/usr/bin/ld: python_dataplane.cc:(.text+0x5c4): undefined reference to
`PyDict_GetItem'
…On Thu, Mar 24, 2022 at 8:01 PM George McCabe ***@***.***> wrote:
I know MET has been built using Python 3.8. We typically advice users to
use the python3-config command to generate the values to set for
MET_PYTHON_LD and MET_PYTHON_CC. If using bash:
export MET_PYTHON_LD="$(python3-config --ldflags)"
export MET_PYTHON_CC="$(python3-config --cflags)"
These values may need to be slightly modified depending on what is output,
but it is a good start. Just make sure that the python3-config command
corresponds to the same version of python3 that you want to use for the
build.
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Can you show how you set |
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these are my main settings on the mac not the ubuntu machine:
export TEST_BASE=/Users/sarr/MET101
export COMPILER=gnu
export MET_SUBDIR=${TEST_BASE}
export MET_TARBALL=met-10.1.0.20220314.tar.gz
export USE_MODULES=FALSE
export MET_PYTHON=/usr/local
export MET_PYTHON_CC=-I/usr/local/anaconda3/include/python3.8
export MET_PYTHON_LD=-L/usr/local/anaconda3/lib/python3.8/config-3.8-darwin
export SET_D64BIT=FALSE
export EXTERNAL_LIBS=/Users/sarr/MET101/external_libs
export MET_GSL=${EXTERNAL_LIBS}/bin
export MET_BUFRLIB=${EXTERNAL_LIBS}/lib
export BUFRLIB_NAME=-lbufr
export MET_NETCDF=${EXTERNAL_LIBS}/bin
export MET_HDF5=${EXTERNAL_LIBS}/bin
export MET_GRIB2CLIBS=${EXTERNAL_LIBS}/lib
export MET_GRIB2CINC=${EXTERNAL_LIBS}/include
export GRIB2CLIB_NAME=-lgrib2c
export LIB_JASPER=${EXTERNAL_LIBS}/lib
export LIB_LIBPNG=${EXTERNAL_LIBS}/lib
export LIB_Z=${EXTERNAL_LIBS}/lib
…On Mon, Mar 28, 2022 at 4:16 PM Kyle Gerheiser ***@***.***> wrote:
Can you show how you set MET_PYTHON_LD? libpython is not being linked
correctly.
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You have the location of the library with
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Hi @fipoucat, were you able to get MET installed? Please let me know if you are still having issues. @kgerheiser, we have applied a fix to get MET to compile using GCC 9. The change has been made in the main_v10.1 branch (dtcenter/MET#2134). We will be creating a bugfix release (MET 10.1.1) this month. |
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Hi @kgerheiser <https://github.com/kgerheiser>, @george, I'll try with this
branch and will update you. Thank you again for the support.
…On Tue, Apr 12, 2022 at 3:57 PM George McCabe ***@***.***> wrote:
Hi @fipoucat <https://github.com/fipoucat>, were you able to get MET
installed? Please let me know if you are still having issues.
@kgerheiser <https://github.com/kgerheiser>, we have applied a fix to get
MET to compile using GCC 9. The change has been made in the main_v10.1
branch (dtcenter/MET#2134 <dtcenter/MET#2134>).
We will be creating a bugfix release (MET 10.1.1) this month.
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still not lucky with the install process using the version 10.1.1 branch 20220419 /usr/bin/ld: ../../../../src/libcode/vx_python3_utils/libvx_python3_utils.a(libvx_python3_utils_a-python3_script.o): in function |
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Show how you have |
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export MET_PYTHON_LD =-L/usr/lib/python3.8 |
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Hi @fipoucat. For MET_PYTHON_LD you'll need the directory containing the python library file and indicate the name of that file. For example: MET_PYTHON_LD='-L/usr/lib/python3.8/config-x86_64-linux-gnu -lpython3.8m' There may need to be other libraries included as well (with -l). You will likely be able to get the information you need by running:
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I am getting the same error with the full setting: error message below, sorry for the length: -Wl,-rpath,/home/sarr/MET101/external_libs/lib:/home/sarr/MET101/external_libs/lib:/home/sarr/MET101/external_libs/lib:/home/sarr/MET101/external_libs/lib:/home/sarr/MET101/external_libs/lib:/home/sarr/MET101/external_libs/lib -Wl,-rpath,/home/sarr/MET101/external_libs/lib:/home/sarr/MET101/external_libs/lib -L/home/sarr/MET101/external_libs/lib -L/home/sarr/MET101/external_libs/lib -L/home/sarr/MET101/external_libs/lib -fopenmp -L/home/sarr/MET101/external_libs/lib -L/home/sarr/MET101/external_libs/lib -L/home/sarr/MET101/external_libs/lib -L/usr/lib/python3.8/config-3.8-x86_64-linux-gnu -L/home/sarr/MET101/external_libs/lib -L/home/sarr/MET101/external_libs/lib -o ensemble_stat ensemble_stat-ensemble_stat.o ensemble_stat-ensemble_stat_conf_info.o -lvx_stat_out -lvx_statistics -lvx_shapedata -lvx_gsl_prob -lvx_analysis_util -lvx_data2d_factory -lvx_data2d_nc_met -lvx_data2d_grib -lvx_data2d_grib2 -lgrib2c -ljasper -lpng -lz -lvx_data2d_nc_pinterp -lvx_data2d_nccf -lvx_data2d_python -lvx_pointdata_python -lvx_python3_utils -L/usr/lib/python3.8/config-3.8-x86_64-linux-gnu -lvx_data2d -lvx_nc_obs -lvx_nc_util -lvx_regrid -lvx_grid -lvx_config -lvx_color -lvx_util -lvx_math -lvx_cal -lvx_log -lvx_data2d_python -lvx_pointdata_python -lvx_python3_utils -L/usr/lib/python3.8/config-3.8-x86_64-linux-gnu -lm -lnetcdf_c++4 -lnetcdf -lgsl -lgslcblas -lhdf5_hl -lhdf5 -lz |
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Hi @fipoucat. You must include the python library file with "-l", which is missing from what you currently have:
It will either be python3.8 or python3.8m. You'll have to look here /usr/lib/python3.8/config-3.8-x86_64-linux-gnu to see what it is. If it is python3.8, MET_PYTHON_LD should look like this:
Note the inclusion of "-lpython3.8". Please try it and let us know how it goes. |
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There is still a problem somewhere because with the above change it is giving the same error. Maybe something is wrong with my python even though 3.9 has the same error. |
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We haven't tested with Python 3.9. Do you have an earlier version of Python to try. We have been using 3.6. |
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I installed an older version but the config is different because python3.6-config --ldflags not a recognized command |
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Hi @fipoucat. My apologies for the delayed response. Somehow I missed your last message. Having python3.6-config isn't essential. All you need to know is where to find the library file so that you can get the path for -L. The extra libs are typically the same and you would likely have the following (replacing with the actual path to the library file):
But, you can install python3.6-config by getting the python3.6-dev package as indicated here: https://command-not-found.com/python3.6-config |
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Hi @jprestop. I spent some time shifting and installed Debian, just an hour
ago I managed now to install MET. I was trying to install gfdl vortex
tracker and unfortunately, it compiles with intel compiler I don't have,
using gnu.
Tomorrow I'll install Metplus without this vortex tracker and hope it will
work.
Many thanks for the support
…On Mon, May 2, 2022 at 8:24 PM jprestop ***@***.***> wrote:
Hi @fipoucat <https://github.com/fipoucat>. My apologies for the delayed
response. Somehow I missed your last message. Having python3.5-config isn't
essential. All you need to know is where to find the library file so that
you can get the path for -L. The extra libs are typically the same and you
would likely have the following (replacing with the actual path to the
library file):
export MET_PYTHON_LD=-L -lpython3.8 -lcrypt-lpthread -ldl -lutil -lm
But, you can install python3.6-config by getting the python3.6-dev package
as indicated here: https://command-not-found.com/python3.6-config
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Hi @fipoucat. I just wanted to follow up. Were you able to get a successful installation? |
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Yes, I manage to install it on the Debian Linux, both MET (35 binaries
created) and MetPlus. The only problem I have is the installation with
vortex tracker which only compile with Intel compiler. Unfortunately
I can only use GNU which is free.
…On Tue, May 17, 2022 at 4:19 PM jprestop ***@***.***> wrote:
Hi @fipoucat <https://github.com/fipoucat>. I just wanted to follow up.
Were you able to get a successful installation?
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I'm glad to hear you were able to get MET and METplus installed, but I'm sorry to hear about your trouble with the vortex tracker. That's a shame that it will only compile with Intel. I'd like to mark this discussion as being answered and "lock it" to prevent future posts. That's how we encourage users to create new discussions for new questions. But I wanted to give you an opportunity to comment on it and/or select the answer yourself, before doing so. Please feel free to select one of the responses as being the best answer to your original question. That'll help future users with similar questions find answers. |
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Hi @fipoucat. I did not realize that when you said the vortex tracker you were likely referring to the GFDL vortex tracker in METplus. A colleague of mine pointed this out and explained that the GFDL vortex tracker in METplus is completely optional and is only used in a few use cases. It is likely that you will never need to use it. However, if you do end up needing it, please start a new discussion and we'll see what we can do to help. And, just so the above message doesn't get lost after this one, I'd like to mark this discussion as being answered and "lock it" to prevent future posts. That's how we encourage users to create new discussions for new questions. But I wanted to give you an opportunity to comment on it and/or select the answer yourself, before doing so. Please feel free to select one of the responses as being the best answer to your original question. That'll help future users with similar questions find answers. |
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Hi @fipoucat.
You must include the python library file with "-l", which is missing from what you currently have:
It will either be python3.8 or python3.8m. You'll have to look here /usr/lib/python3.8/config-3.8-x86_64-linux-gnu to see what it is. If it is python3.8, MET_PYTHON_LD should look like this:
Note the inclusion of "-lpython3.8". Please try it and let us know how it goes.