GLIB error importing conda package

[Richard Signell]

Conda folks,

We successfully built Iris as a conda module on Linux64 and have successfully installed it on several linux 64 anaconda machines via:

conda install -c rsignell iris==1.7.0_dev_395c61d

but on Wakari (np18py27-1.9), although it installs, when I try to import it (import iris), I get:

ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /opt/anaconda/envs/np18py27-1.9/lib/python2.7/site-packages/cartopy/trace.so)

Any idea how to fix this?

-Rich

[Ilan Schnell]

It looks like the C++ runtime library on the Wakari system is incompatible
with the build of Iris. Which system is Wakari running on? What is
/etc/issue.

Thanks Ilan

Post by Richard Signell
Conda folks,
conda install -c rsignell iris==1.7.0_dev_395c61d
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /opt/anaconda/envs/np18py27-1.9/lib/python2.7/site-packages/cartopy/trace.so)
Any idea how to fix this?
-Rich
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[Trent Nelson]

Just to further what Ilan said, I would expect to see this if I conda built on a newer version of Linux (with a later glibc), then tried to run that binary on an older version.

I think wakari is centos 6.x.

We build all our official anaconda packages on centos 5 to avoid this.

@Sean: what version of Linux do the binstar builders run? Richard: you could try building via binstar.

Sent from my iPhone

It looks like the C++ runtime library on the Wakari system is incompatible with the build of Iris. Which system is Wakari running on? What is /etc/issue.
Thanks Ilan

Post by Richard Signell
Conda folks,
conda install -c rsignell iris==1.7.0_dev_395c61d
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /opt/anaconda/envs/np18py27-1.9/lib/python2.7/site-packages/cartopy/trace.so)
Any idea how to fix this?
-Rich
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[Filipe Pires Alvarenga Fernandes]

Post by Trent Nelson
Just to further what Ilan said, I would expect to see this if I conda
built on a newer version of Linux (with a later glibc), then tried to run
that binary on an older version.
I think wakari is centos 6.x.
We build all our official anaconda packages on centos 5 to avoid this.
@Sean: what version of Linux do the binstar builders run? Richard: you
could try building via binstar.

Hi Trent,

I am having the same issue. I was using conda build inside my wakari shell
as a work around to that problem, but you mentioned building it via
binstar. Can you point me to the docs on how to do that?

Thanks,

-Filipe

Post by Trent Nelson
Sent from my iPhone
It looks like the C++ runtime library on the Wakari system is incompatible
with the build of Iris. Which system is Wakari running on? What is
/etc/issue.
Thanks Ilan

Post by Richard Signell
Conda folks,
conda install -c rsignell iris==1.7.0_dev_395c61d
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /opt/anaconda/envs/np18py27-1.9/lib/python2.7/site-packages/cartopy/trace.so)
Any idea how to fix this?
-Rich
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[Work]

Hi Ilan Hi Trent,

The GLIBC issue seems to be a recurring issue in many packages.

Here is a link to a discussion I started on the WxPython group that has a similar error:

https://groups.google.com/forum/m/#!topic/wx-users/75mT1NpbbBo

From what I am reading, I understand that different Linux distributions carry different libraries compiled differently. In other words, there are multiple versions of code for Linux. Therefore there may be a need to allow multiple Linux binaries built for multiple platforms. If I understand this correctly, this can result in a ridiculous number of binary versions. Please correct me if I am wrong.

One solution I saw quoted by people is building against older versions of libraries. Yet there are compatibility issues with this I encountered. Is there any other way, such as somehow bringing newer dependent libraries into anaconda as part of the package installation? Does it make sense at all?

I hope someone can help resolve this and that there is a resolution.

Jacob


Sent from my iPhone

Post by Trent Nelson
Just to further what Ilan said, I would expect to see this if I conda built on a newer version of Linux (with a later glibc), then tried to run that binary on an older version.
I think wakari is centos 6.x.
We build all our official anaconda packages on centos 5 to avoid this.
@Sean: what version of Linux do the binstar builders run? Richard: you could try building via binstar.

Hi Trent,
I am having the same issue. I was using conda build inside my wakari shell as a work around to that problem, but you mentioned building it via binstar. Can you point me to the docs on how to do that?
Thanks,
-Filipe

Post by Trent Nelson
Sent from my iPhone

It looks like the C++ runtime library on the Wakari system is incompatible with the build of Iris. Which system is Wakari running on? What is /etc/issue.
Thanks Ilan

Post by Richard Signell
Conda folks,
conda install -c rsignell iris==1.7.0_dev_395c61d
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /opt/anaconda/envs/np18py27-1.9/lib/python2.7/site-packages/cartopy/trace.so)
Any idea how to fix this?
-Rich
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[Aaron Meurer]

There have been discussions on building a libc conda package, but it's
not clear if it will work, or how easy it will be to do.

Aaron Meurer

Post by Work
Hi Ilan Hi Trent,
The GLIBC issue seems to be a recurring issue in many packages.
https://groups.google.com/forum/m/#!topic/wx-users/75mT1NpbbBo
From what I am reading, I understand that different Linux distributions
carry different libraries compiled differently. In other words, there are
multiple versions of code for Linux. Therefore there may be a need to allow
multiple Linux binaries built for multiple platforms. If I understand this
correctly, this can result in a ridiculous number of binary versions. Please
correct me if I am wrong.
One solution I saw quoted by people is building against older versions of
libraries. Yet there are compatibility issues with this I encountered. Is
there any other way, such as somehow bringing newer dependent libraries into
anaconda as part of the package installation? Does it make sense at all?
I hope someone can help resolve this and that there is a resolution.
Jacob
Sent from my iPhone
On Jul 10, 2014, at 10:11 AM, Filipe Pires Alvarenga Fernandes

Post by Trent Nelson
Just to further what Ilan said, I would expect to see this if I conda
built on a newer version of Linux (with a later glibc), then tried to run
that binary on an older version.
I think wakari is centos 6.x.
We build all our official anaconda packages on centos 5 to avoid this.
@Sean: what version of Linux do the binstar builders run? Richard: you
could try building via binstar.

Hi Trent,
I am having the same issue. I was using conda build inside my wakari shell
as a work around to that problem, but you mentioned building it via
binstar. Can you point me to the docs on how to do that?
Thanks,
-Filipe

Post by Trent Nelson
Sent from my iPhone
It looks like the C++ runtime library on the Wakari system is incompatible
with the build of Iris. Which system is Wakari running on? What is
/etc/issue.
Thanks Ilan

Post by Richard Signell
Conda folks,
We successfully built Iris as a conda module on Linux64 and have
conda install -c rsignell iris==1.7.0_dev_395c61d
but on Wakari (np18py27-1.9), although it installs, when I try to import
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not
found (required by
/opt/anaconda/envs/np18py27-1.9/lib/python2.7/site-packages/cartopy/trace.so)
Any idea how to fix this?
-Rich
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[Filipe Pires Alvarenga Fernandes]

Aaron, when you mentioned "build it at binstar" to Signell I thought that
there was a build service in the same fashion as OBS (
https://build.opensuse.org/). Where we have some architecture/distro
options for building (or maybe even just one that is compatible with
wakari) . IMHO I think that building binaries locally and uploading can be
quite confusing, and may lead to a world of pain. On the other hand, it
does safe a lot of time for those who know what they are doing...

-Filipe

Post by Aaron Meurer
There have been discussions on building a libc conda package, but it's
not clear if it will work, or how easy it will be to do.
Aaron Meurer

Post by Work
Hi Ilan Hi Trent,
The GLIBC issue seems to be a recurring issue in many packages.
Here is a link to a discussion I started on the WxPython group that has a
https://groups.google.com/forum/m/#!topic/wx-users/75mT1NpbbBo
From what I am reading, I understand that different Linux distributions
carry different libraries compiled differently. In other words, there are
multiple versions of code for Linux. Therefore there may be a need to

allow

Post by Work
multiple Linux binaries built for multiple platforms. If I understand

this

Post by Work
correctly, this can result in a ridiculous number of binary versions.

Please

Post by Work
correct me if I am wrong.
One solution I saw quoted by people is building against older versions of
libraries. Yet there are compatibility issues with this I encountered. Is
there any other way, such as somehow bringing newer dependent libraries

into

Post by Work
anaconda as part of the package installation? Does it make sense at all?
I hope someone can help resolve this and that there is a resolution.
Jacob
Sent from my iPhone
On Jul 10, 2014, at 10:11 AM, Filipe Pires Alvarenga Fernandes

Post by Trent Nelson
Just to further what Ilan said, I would expect to see this if I conda
built on a newer version of Linux (with a later glibc), then tried to

run

Post by Work

Post by Trent Nelson
that binary on an older version.
I think wakari is centos 6.x.
We build all our official anaconda packages on centos 5 to avoid this.
@Sean: what version of Linux do the binstar builders run? Richard: you
could try building via binstar.

Hi Trent,
I am having the same issue. I was using conda build inside my wakari

shell

Post by Work
as a work around to that problem, but you mentioned building it via
binstar. Can you point me to the docs on how to do that?
Thanks,
-Filipe

Post by Trent Nelson
Sent from my iPhone
It looks like the C++ runtime library on the Wakari system is

incompatible

Post by Work

Post by Trent Nelson
with the build of Iris. Which system is Wakari running on? What is
/etc/issue.
Thanks Ilan

Post by Richard Signell
Conda folks,
We successfully built Iris as a conda module on Linux64 and have
conda install -c rsignell iris==1.7.0_dev_395c61d
but on Wakari (np18py27-1.9), although it installs, when I try to

import

Post by Work

Post by Trent Nelson

Post by Richard Signell
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not
found (required by

/opt/anaconda/envs/np18py27-1.9/lib/python2.7/site-packages/cartopy/trace.so)

Post by Work

Post by Trent Nelson

Post by Richard Signell
Any idea how to fix this?
-Rich
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Post by Work

Post by Trent Nelson

Post by Richard Signell
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an

Post by Work

Post by Trent Nelson

Post by Richard Signell
Visit this group at

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Post by Work

Post by Trent Nelson
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Post by Work

Post by Trent Nelson
Visit this group at

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Post by Work

Post by Trent Nelson
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Post by Work
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[Aaron Meurer]

We do have a build service in the works, but it is not publicly available yet.

Aaron Meurer

On Wed, Jul 16, 2014 at 6:21 PM, Filipe Pires Alvarenga Fernandes

Post by Filipe Pires Alvarenga Fernandes
Aaron, when you mentioned "build it at binstar" to Signell I thought that
there was a build service in the same fashion as OBS
(https://build.opensuse.org/). Where we have some architecture/distro
options for building (or maybe even just one that is compatible with wakari)
. IMHO I think that building binaries locally and uploading can be quite
confusing, and may lead to a world of pain. On the other hand, it does safe
a lot of time for those who know what they are doing...
-Filipe

Post by Aaron Meurer
There have been discussions on building a libc conda package, but it's
not clear if it will work, or how easy it will be to do.
Aaron Meurer

Post by Work
Hi Ilan Hi Trent,
The GLIBC issue seems to be a recurring issue in many packages.
Here is a link to a discussion I started on the WxPython group that has a
https://groups.google.com/forum/m/#!topic/wx-users/75mT1NpbbBo
From what I am reading, I understand that different Linux distributions
carry different libraries compiled differently. In other words, there are
multiple versions of code for Linux. Therefore there may be a need to allow
multiple Linux binaries built for multiple platforms. If I understand this
correctly, this can result in a ridiculous number of binary versions. Please
correct me if I am wrong.
One solution I saw quoted by people is building against older versions of
libraries. Yet there are compatibility issues with this I encountered. Is
there any other way, such as somehow bringing newer dependent libraries into
anaconda as part of the package installation? Does it make sense at all?
I hope someone can help resolve this and that there is a resolution.
Jacob
Sent from my iPhone
On Jul 10, 2014, at 10:11 AM, Filipe Pires Alvarenga Fernandes

Post by Trent Nelson
Just to further what Ilan said, I would expect to see this if I conda
built on a newer version of Linux (with a later glibc), then tried to run
that binary on an older version.
I think wakari is centos 6.x.
We build all our official anaconda packages on centos 5 to avoid this.
@Sean: what version of Linux do the binstar builders run? Richard: you
could try building via binstar.

Hi Trent,
I am having the same issue. I was using conda build inside my wakari shell
as a work around to that problem, but you mentioned building it via
binstar. Can you point me to the docs on how to do that?
Thanks,
-Filipe

Post by Trent Nelson
Sent from my iPhone
It looks like the C++ runtime library on the Wakari system is incompatible
with the build of Iris. Which system is Wakari running on? What is
/etc/issue.
Thanks Ilan

Post by Richard Signell
Conda folks,
We successfully built Iris as a conda module on Linux64 and have
conda install -c rsignell iris==1.7.0_dev_395c61d
but on Wakari (np18py27-1.9), although it installs, when I try to import
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not
found (required by
/opt/anaconda/envs/np18py27-1.9/lib/python2.7/site-packages/cartopy/trace.so)
Any idea how to fix this?
-Rich
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[Filipe Pires Alvarenga Fernandes]

Cool, looking forward to it!

Post by Aaron Meurer
We do have a build service in the works, but it is not publicly available yet.
Aaron Meurer
On Wed, Jul 16, 2014 at 6:21 PM, Filipe Pires Alvarenga Fernandes

Post by Filipe Pires Alvarenga Fernandes
Aaron, when you mentioned "build it at binstar" to Signell I thought that
there was a build service in the same fashion as OBS
(https://build.opensuse.org/). Where we have some architecture/distro
options for building (or maybe even just one that is compatible with

wakari)

Post by Filipe Pires Alvarenga Fernandes
. IMHO I think that building binaries locally and uploading can be quite
confusing, and may lead to a world of pain. On the other hand, it does

safe

Post by Filipe Pires Alvarenga Fernandes
a lot of time for those who know what they are doing...
-Filipe

Post by Aaron Meurer
There have been discussions on building a libc conda package, but it's
not clear if it will work, or how easy it will be to do.
Aaron Meurer

Post by Work
Hi Ilan Hi Trent,
The GLIBC issue seems to be a recurring issue in many packages.
Here is a link to a discussion I started on the WxPython group that

has

Post by Filipe Pires Alvarenga Fernandes

Post by Aaron Meurer

Post by Work
a
https://groups.google.com/forum/m/#!topic/wx-users/75mT1NpbbBo
From what I am reading, I understand that different Linux

distributions

Post by Filipe Pires Alvarenga Fernandes

Post by Aaron Meurer

Post by Work
carry different libraries compiled differently. In other words, there are
multiple versions of code for Linux. Therefore there may be a need to allow
multiple Linux binaries built for multiple platforms. If I understand this
correctly, this can result in a ridiculous number of binary versions. Please
correct me if I am wrong.
One solution I saw quoted by people is building against older versions of
libraries. Yet there are compatibility issues with this I encountered. Is
there any other way, such as somehow bringing newer dependent

libraries

Post by Filipe Pires Alvarenga Fernandes

Post by Aaron Meurer

Post by Work
into
anaconda as part of the package installation? Does it make sense at

all?

Post by Filipe Pires Alvarenga Fernandes

Post by Aaron Meurer

Post by Work
I hope someone can help resolve this and that there is a resolution.
Jacob
Sent from my iPhone
On Jul 10, 2014, at 10:11 AM, Filipe Pires Alvarenga Fernandes
On Tue, Jul 8, 2014 at 3:10 PM, Trent Nelson <

Post by Trent Nelson
Just to further what Ilan said, I would expect to see this if I conda
built on a newer version of Linux (with a later glibc), then tried to run
that binary on an older version.
I think wakari is centos 6.x.
We build all our official anaconda packages on centos 5 to avoid

this.
you

Post by Filipe Pires Alvarenga Fernandes

Post by Aaron Meurer

Post by Work

Post by Trent Nelson
could try building via binstar.

Hi Trent,
I am having the same issue. I was using conda build inside my wakari shell
as a work around to that problem, but you mentioned building it via
binstar. Can you point me to the docs on how to do that?
Thanks,
-Filipe

Post by Trent Nelson
Sent from my iPhone
It looks like the C++ runtime library on the Wakari system is incompatible
with the build of Iris. Which system is Wakari running on? What is
/etc/issue.
Thanks Ilan

Post by Richard Signell
Conda folks,
We successfully built Iris as a conda module on Linux64 and have
conda install -c rsignell iris==1.7.0_dev_395c61d
but on Wakari (np18py27-1.9), although it installs, when I try to import
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not
found (required by

/opt/anaconda/envs/np18py27-1.9/lib/python2.7/site-packages/cartopy/trace.so)

Post by Filipe Pires Alvarenga Fernandes

Post by Aaron Meurer

Post by Work

Post by Trent Nelson

Post by Richard Signell
Any idea how to fix this?
-Rich
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[Work]

Hi Aaron,

Is there a possibility of a partial GLIB solution before you have a build service ready and running? Something at the level of guidelines on how to build a package for anaconda?

Specific to the issue I mentioned, I want my package to work with the same libraries anaconda 2.01 is delivered with. So when I compile it I wish to use the libraries anaconda uses after a fresh install. There should be a way to do this.

I will take Ubuntu 14.04 LTS as an example. Upon a fresh install and importing libraries needed to compile WxPython the libm.so.6 file points to libm-2.19.so while the anaconda install uses libm-2.5.so. I assume that since WxPython is compiled against the former and ran against the latter it results in the incompatibility issue.

Is there a way to tell the Package build process to use the anaconda libraries rather than the Linux default libraries? I want my code to run on the same anaconda version and same Linux version I built the library in. I was thinking of changing the libm.so.6 link to point to the anaconda library before the build, yet there should be a more elegant way. For example, is it possible to install the same libraries that anaconda uses on Linux so the libraries will match and then build the package. Is this more elegant? Will it work? If yes, what environment should I have to match anaconda? What Linux packages should I install?

If I understand, this is part of the build service environment you plan to offer, yet is there anything that can be done before such a service is available?

I hope there is a solution close at hand.

Jacob



Sent from my iPhone

Post by Aaron Meurer
There have been discussions on building a libc conda package, but it's
not clear if it will work, or how easy it will be to do.
Aaron Meurer

Post by Work
Hi Ilan Hi Trent,
The GLIBC issue seems to be a recurring issue in many packages.
https://groups.google.com/forum/m/#!topic/wx-users/75mT1NpbbBo
From what I am reading, I understand that different Linux distributions
carry different libraries compiled differently. In other words, there are
multiple versions of code for Linux. Therefore there may be a need to allow
multiple Linux binaries built for multiple platforms. If I understand this
correctly, this can result in a ridiculous number of binary versions. Please
correct me if I am wrong.
One solution I saw quoted by people is building against older versions of
libraries. Yet there are compatibility issues with this I encountered. Is
there any other way, such as somehow bringing newer dependent libraries into
anaconda as part of the package installation? Does it make sense at all?
I hope someone can help resolve this and that there is a resolution.
Jacob
Sent from my iPhone
On Jul 10, 2014, at 10:11 AM, Filipe Pires Alvarenga Fernandes

Post by Trent Nelson
Just to further what Ilan said, I would expect to see this if I conda
built on a newer version of Linux (with a later glibc), then tried to run
that binary on an older version.
I think wakari is centos 6.x.
We build all our official anaconda packages on centos 5 to avoid this.
@Sean: what version of Linux do the binstar builders run? Richard: you
could try building via binstar.

Hi Trent,
I am having the same issue. I was using conda build inside my wakari shell
as a work around to that problem, but you mentioned building it via
binstar. Can you point me to the docs on how to do that?
Thanks,
-Filipe

Post by Trent Nelson
Sent from my iPhone
It looks like the C++ runtime library on the Wakari system is incompatible
with the build of Iris. Which system is Wakari running on? What is
/etc/issue.
Thanks Ilan

Post by Richard Signell
Conda folks,
We successfully built Iris as a conda module on Linux64 and have
conda install -c rsignell iris==1.7.0_dev_395c61d
but on Wakari (np18py27-1.9), although it installs, when I try to import
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not
found (required by
/opt/anaconda/envs/np18py27-1.9/lib/python2.7/site-packages/cartopy/trace.so)
Any idea how to fix this?
-Rich
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[Aaron Meurer]

Anaconda doesn't ship with libm or glibc. Your best bet is to compile
your packages on CentOS 5, which is the same OS we compile our
packages with.

Aaron Meurer

Post by Work
Hi Aaron,
Is there a possibility of a partial GLIB solution before you have a build service ready and running? Something at the level of guidelines on how to build a package for anaconda?
Specific to the issue I mentioned, I want my package to work with the same libraries anaconda 2.01 is delivered with. So when I compile it I wish to use the libraries anaconda uses after a fresh install. There should be a way to do this.
I will take Ubuntu 14.04 LTS as an example. Upon a fresh install and importing libraries needed to compile WxPython the libm.so.6 file points to libm-2.19.so while the anaconda install uses libm-2.5.so. I assume that since WxPython is compiled against the former and ran against the latter it results in the incompatibility issue.
Is there a way to tell the Package build process to use the anaconda libraries rather than the Linux default libraries? I want my code to run on the same anaconda version and same Linux version I built the library in. I was thinking of changing the libm.so.6 link to point to the anaconda library before the build, yet there should be a more elegant way. For example, is it possible to install the same libraries that anaconda uses on Linux so the libraries will match and then build the package. Is this more elegant? Will it work? If yes, what environment should I have to match anaconda? What Linux packages should I install?
If I understand, this is part of the build service environment you plan to offer, yet is there anything that can be done before such a service is available?
I hope there is a solution close at hand.
Jacob
Sent from my iPhone

Post by Aaron Meurer
There have been discussions on building a libc conda package, but it's
not clear if it will work, or how easy it will be to do.
Aaron Meurer

Post by Work
Hi Ilan Hi Trent,
The GLIBC issue seems to be a recurring issue in many packages.
Here is a link to a discussion I started on the WxPython group that has a
https://groups.google.com/forum/m/#!topic/wx-users/75mT1NpbbBo
From what I am reading, I understand that different Linux distributions
carry different libraries compiled differently. In other words, there are
multiple versions of code for Linux. Therefore there may be a need to allow
multiple Linux binaries built for multiple platforms. If I understand this
correctly, this can result in a ridiculous number of binary versions. Please
correct me if I am wrong.
One solution I saw quoted by people is building against older versions of
libraries. Yet there are compatibility issues with this I encountered. Is
there any other way, such as somehow bringing newer dependent libraries into
anaconda as part of the package installation? Does it make sense at all?
I hope someone can help resolve this and that there is a resolution.
Jacob
Sent from my iPhone
On Jul 10, 2014, at 10:11 AM, Filipe Pires Alvarenga Fernandes

Post by Trent Nelson
Just to further what Ilan said, I would expect to see this if I conda
built on a newer version of Linux (with a later glibc), then tried to run
that binary on an older version.
I think wakari is centos 6.x.
We build all our official anaconda packages on centos 5 to avoid this.
@Sean: what version of Linux do the binstar builders run? Richard: you
could try building via binstar.

Hi Trent,
I am having the same issue. I was using conda build inside my wakari shell
as a work around to that problem, but you mentioned building it via
binstar. Can you point me to the docs on how to do that?
Thanks,
-Filipe

Post by Trent Nelson
Sent from my iPhone
It looks like the C++ runtime library on the Wakari system is incompatible
with the build of Iris. Which system is Wakari running on? What is
/etc/issue.
Thanks Ilan

Post by Richard Signell
Conda folks,
We successfully built Iris as a conda module on Linux64 and have
conda install -c rsignell iris==1.7.0_dev_395c61d
but on Wakari (np18py27-1.9), although it installs, when I try to import
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not
found (required by
/opt/anaconda/envs/np18py27-1.9/lib/python2.7/site-packages/cartopy/trace.so)
Any idea how to fix this?
-Rich
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[Trent Nelson]

Hey Jacob can you point us at the WxPython recipe you've got going so far?

I may be able to find some time to take a crack at it this week.

Post by Work
Hi Aaron,
Is there a possibility of a partial GLIB solution before you have a build service ready and running? Something at the level of guidelines on how to build a package for anaconda?
Specific to the issue I mentioned, I want my package to work with the same libraries anaconda 2.01 is delivered with. So when I compile it I wish to use the libraries anaconda uses after a fresh install. There should be a way to do this.
I will take Ubuntu 14.04 LTS as an example. Upon a fresh install and importing libraries needed to compile WxPython the libm.so.6 file points to libm-2.19.so while the anaconda install uses libm-2.5.so. I assume that since WxPython is compiled against the former and ran against the latter it results in the incompatibility issue.
Is there a way to tell the Package build process to use the anaconda libraries rather than the Linux default libraries? I want my code to run on the same anaconda version and same Linux version I built the library in. I was thinking of changing the libm.so.6 link to point to the anaconda library before the build, yet there should be a more elegant way. For example, is it possible to install the same libraries that anaconda uses on Linux so the libraries will match and then build the package. Is this more elegant? Will it work? If yes, what environment should I have to match anaconda? What Linux packages should I install?
If I understand, this is part of the build service environment you plan to offer, yet is there anything that can be done before such a service is available?
I hope there is a solution close at hand.
Jacob
Sent from my iPhone

Post by Aaron Meurer
There have been discussions on building a libc conda package, but it's
not clear if it will work, or how easy it will be to do.
Aaron Meurer

Post by Work
Hi Ilan Hi Trent,
The GLIBC issue seems to be a recurring issue in many packages.
Here is a link to a discussion I started on the WxPython group that has a
https://groups.google.com/forum/m/#!topic/wx-users/75mT1NpbbBo
From what I am reading, I understand that different Linux distributions
carry different libraries compiled differently. In other words, there are
multiple versions of code for Linux. Therefore there may be a need to allow
multiple Linux binaries built for multiple platforms. If I understand this
correctly, this can result in a ridiculous number of binary versions. Please
correct me if I am wrong.
One solution I saw quoted by people is building against older versions of
libraries. Yet there are compatibility issues with this I encountered. Is
there any other way, such as somehow bringing newer dependent libraries into
anaconda as part of the package installation? Does it make sense at all?
I hope someone can help resolve this and that there is a resolution.
Jacob
Sent from my iPhone
On Jul 10, 2014, at 10:11 AM, Filipe Pires Alvarenga Fernandes

Post by Trent Nelson
Just to further what Ilan said, I would expect to see this if I conda
built on a newer version of Linux (with a later glibc), then tried to run
that binary on an older version.
I think wakari is centos 6.x.
We build all our official anaconda packages on centos 5 to avoid this.
@Sean: what version of Linux do the binstar builders run? Richard: you
could try building via binstar.

Hi Trent,
I am having the same issue. I was using conda build inside my wakari shell
as a work around to that problem, but you mentioned building it via
binstar. Can you point me to the docs on how to do that?
Thanks,
-Filipe

Post by Trent Nelson
Sent from my iPhone
It looks like the C++ runtime library on the Wakari system is incompatible
with the build of Iris. Which system is Wakari running on? What is
/etc/issue.
Thanks Ilan

Post by Richard Signell
Conda folks,
We successfully built Iris as a conda module on Linux64 and have
conda install -c rsignell iris==1.7.0_dev_395c61d
but on Wakari (np18py27-1.9), although it installs, when I try to import
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not
found (required by
/opt/anaconda/envs/np18py27-1.9/lib/python2.7/site-packages/cartopy/trace.so)
Any idea how to fix this?
-Rich
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[Jacob Barhak]

Thanks Trent,

Your offer is appreciated.

You will find attached a zip file with the build.sh and meta.yaml. the
meta.yaml is a copy of what Travis and Aaron did and is available on
binstar. build.sh is a bit different since WxPython 3.0 now has its own
build script.

I have an Ubuntu VM where it builds yet does not run with the GLIBC issue.

Also, before running the conda build you will need to do the following:

sudo apt-get install mesa-common-dev libgl1-mesa-glx libglu1-mesa
libgl1-mesa-dev libglu1-mesa-dev libgstreamer0.10-dev libgconf2-dev
libsdl1.2-dev zlib1g-dev libjpeg62-dev python-gst0.10-dev libgtk2.0-dev

When I ran this, I created a condabuild directory under WxPython and
launched conda build from there - yet may want to perform the modifications
needed in the build command.

Finally. note that WxPython build does work on Ubuntu 14.04 without
anaconda to the degree that the demo runs. So the issue is
Ubuntu+Anaconda+WxPythonand specifically the libraries.

While you try to improve this, I will try building on CentOs7. Aaron
recommended version 5, yet if version 7 is already out I and does not
match this issue will have to gain priority if you want to support multiple
Linux platforms for multiple packages.

I hope at least one stable solution can be found.

Jacob

Hey Jacob can you point us at the WxPython recipe you’ve got going so far?
I may be able to find some time to take a crack at it this week.

Post by Work
Hi Aaron,
Is there a possibility of a partial GLIB solution before you have a

build service ready and running? Something at the level of guidelines on
how to build a package for anaconda?

Post by Work
Specific to the issue I mentioned, I want my package to work with the

same libraries anaconda 2.01 is delivered with. So when I compile it I wish
to use the libraries anaconda uses after a fresh install. There should be a
way to do this.

Post by Work
I will take Ubuntu 14.04 LTS as an example. Upon a fresh install and

importing libraries needed to compile WxPython the libm.so.6 file points to
libm-2.19.so while the anaconda install uses libm-2.5.so. I assume that
since WxPython is compiled against the former and ran against the latter it
results in the incompatibility issue.

Post by Work
Is there a way to tell the Package build process to use the anaconda

libraries rather than the Linux default libraries? I want my code to run on
the same anaconda version and same Linux version I built the library in. I
was thinking of changing the libm.so.6 link to point to the anaconda
library before the build, yet there should be a more elegant way. For
example, is it possible to install the same libraries that anaconda uses on
Linux so the libraries will match and then build the package. Is this more
elegant? Will it work? If yes, what environment should I have to match
anaconda? What Linux packages should I install?

Post by Work
If I understand, this is part of the build service environment you plan

to offer, yet is there anything that can be done before such a service is
available?

Post by Work
I hope there is a solution close at hand.
Jacob
Sent from my iPhone

Post by Aaron Meurer
There have been discussions on building a libc conda package, but it's
not clear if it will work, or how easy it will be to do.
Aaron Meurer

Post by Work
Hi Ilan Hi Trent,
The GLIBC issue seems to be a recurring issue in many packages.
Here is a link to a discussion I started on the WxPython group that

has a

Post by Work

Post by Aaron Meurer

Post by Work
https://groups.google.com/forum/m/#!topic/wx-users/75mT1NpbbBo
From what I am reading, I understand that different Linux distributions
carry different libraries compiled differently. In other words, there

are

Post by Work

Post by Aaron Meurer

Post by Work
multiple versions of code for Linux. Therefore there may be a need to

allow

Post by Work

Post by Aaron Meurer

Post by Work
multiple Linux binaries built for multiple platforms. If I understand

this

Post by Work

Post by Aaron Meurer

Post by Work
correctly, this can result in a ridiculous number of binary versions.

Please

Post by Work

Post by Aaron Meurer

Post by Work
correct me if I am wrong.
One solution I saw quoted by people is building against older versions

of

Post by Work

Post by Aaron Meurer

Post by Work
libraries. Yet there are compatibility issues with this I encountered.

Is

Post by Work

Post by Aaron Meurer

Post by Work
there any other way, such as somehow bringing newer dependent

libraries into

Post by Work

Post by Aaron Meurer

Post by Work
anaconda as part of the package installation? Does it make sense at

all?

Post by Work

Post by Aaron Meurer

Post by Work
I hope someone can help resolve this and that there is a resolution.
Jacob
Sent from my iPhone
On Jul 10, 2014, at 10:11 AM, Filipe Pires Alvarenga Fernandes
On Tue, Jul 8, 2014 at 3:10 PM, Trent Nelson <

Post by Trent Nelson
Just to further what Ilan said, I would expect to see this if I conda
built on a newer version of Linux (with a later glibc), then tried to

run

Post by Work

Post by Aaron Meurer

Post by Work

Post by Trent Nelson
that binary on an older version.
I think wakari is centos 6.x.
We build all our official anaconda packages on centos 5 to avoid this.

you

Post by Work

Post by Aaron Meurer

Post by Work

Post by Trent Nelson
could try building via binstar.

Hi Trent,
I am having the same issue. I was using conda build inside my wakari

shell

Post by Work

Post by Aaron Meurer

Post by Work
as a work around to that problem, but you mentioned building it via
binstar. Can you point me to the docs on how to do that?
Thanks,
-Filipe

Post by Trent Nelson
Sent from my iPhone
It looks like the C++ runtime library on the Wakari system is

incompatible

Post by Work

Post by Aaron Meurer

Post by Work

Post by Trent Nelson
with the build of Iris. Which system is Wakari running on? What is
/etc/issue.
Thanks Ilan

Post by Richard Signell
Conda folks,
We successfully built Iris as a conda module on Linux64 and have
conda install -c rsignell iris==1.7.0_dev_395c61d
but on Wakari (np18py27-1.9), although it installs, when I try to

import

Post by Work

Post by Aaron Meurer

Post by Work

Post by Trent Nelson

Post by Richard Signell
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not
found (required by

/opt/anaconda/envs/np18py27-1.9/lib/python2.7/site-packages/cartopy/trace.so)

Post by Work

Post by Aaron Meurer

Post by Work

Post by Trent Nelson

Post by Richard Signell
Any idea how to fix this?
-Rich
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Post by Aaron Meurer

Post by Work

Post by Trent Nelson

Post by Richard Signell
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Post by Work

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[Work]

Hi Aaron,

Your suggestion to use CentOS seems to be progress. However, there are still incompatibilities with CentOs7.

The good news are that conda install wxpython works without raising warnings. However, there are still some funny behavior that is incompatible with the windows WxPython.

The bad news are that building WxPython on CentOs7 is far from trivial. Some dependent libraries are not the same as Ubuntu and after several attempts I stopped trying on a gstreamer error while building. I did not even get to the point where GLibC is the issue.

Another issue is that the CentOS 7 repo does not seem to have grid engine, which I need. Perhaps I should downgrade to an earlier version of CentOS. However, I already had things working at almost the same level with Ubuntu 12.04.

Perhaps the issues I am encountering of WxPython not being compatible with the windows behavior is a WxPython issue and the problem is solved for me on Ubuntu 12.04 LTS. Perhaps I should not try to build WxPython at all.

I will explore this option. So Trent, unless you have other reasons to resolve this issue for Ubuntu you may wish to delay trying to rebuild the WxPython conda package. Aaron and Travis did this already and even if you success it may not resolve my issue. I was assuming this is an OS incompatibility issue, yet I may be wrong and have to verify this.

I hope this message saves you some time.

Jacob

Sent from my iPhone

Post by Jacob Barhak
Thanks Trent,
Your offer is appreciated.
You will find attached a zip file with the build.sh and meta.yaml. the meta.yaml is a copy of what Travis and Aaron did and is available on binstar. build.sh is a bit different since WxPython 3.0 now has its own build script.
I have an Ubuntu VM where it builds yet does not run with the GLIBC issue.
sudo apt-get install mesa-common-dev libgl1-mesa-glx libglu1-mesa libgl1-mesa-dev libglu1-mesa-dev libgstreamer0.10-dev libgconf2-dev libsdl1.2-dev zlib1g-dev libjpeg62-dev python-gst0.10-dev libgtk2.0-dev
When I ran this, I created a condabuild directory under WxPython and launched conda build from there - yet may want to perform the modifications needed in the build command.
Finally. note that WxPython build does work on Ubuntu 14.04 without anaconda to the degree that the demo runs. So the issue is Ubuntu+Anaconda+WxPythonand specifically the libraries.
While you try to improve this, I will try building on CentOs7. Aaron recommended version 5, yet if version 7 is already out I and does not match this issue will have to gain priority if you want to support multiple Linux platforms for multiple packages.
I hope at least one stable solution can be found.
Jacob

Hey Jacob can you point us at the WxPython recipe you’ve got going so far?
I may be able to find some time to take a crack at it this week.

Post by Work
Hi Aaron,
Is there a possibility of a partial GLIB solution before you have a build service ready and running? Something at the level of guidelines on how to build a package for anaconda?
Specific to the issue I mentioned, I want my package to work with the same libraries anaconda 2.01 is delivered with. So when I compile it I wish to use the libraries anaconda uses after a fresh install. There should be a way to do this.
I will take Ubuntu 14.04 LTS as an example. Upon a fresh install and importing libraries needed to compile WxPython the libm.so.6 file points to libm-2.19.so while the anaconda install uses libm-2.5.so. I assume that since WxPython is compiled against the former and ran against the latter it results in the incompatibility issue.
Is there a way to tell the Package build process to use the anaconda libraries rather than the Linux default libraries? I want my code to run on the same anaconda version and same Linux version I built the library in. I was thinking of changing the libm.so.6 link to point to the anaconda library before the build, yet there should be a more elegant way. For example, is it possible to install the same libraries that anaconda uses on Linux so the libraries will match and then build the package. Is this more elegant? Will it work? If yes, what environment should I have to match anaconda? What Linux packages should I install?
If I understand, this is part of the build service environment you plan to offer, yet is there anything that can be done before such a service is available?
I hope there is a solution close at hand.
Jacob
Sent from my iPhone

Post by Aaron Meurer
There have been discussions on building a libc conda package, but it's
not clear if it will work, or how easy it will be to do.
Aaron Meurer

Post by Work
Hi Ilan Hi Trent,
The GLIBC issue seems to be a recurring issue in many packages.
Here is a link to a discussion I started on the WxPython group that has a
https://groups.google.com/forum/m/#!topic/wx-users/75mT1NpbbBo
From what I am reading, I understand that different Linux distributions
carry different libraries compiled differently. In other words, there are
multiple versions of code for Linux. Therefore there may be a need to allow
multiple Linux binaries built for multiple platforms. If I understand this
correctly, this can result in a ridiculous number of binary versions. Please
correct me if I am wrong.
One solution I saw quoted by people is building against older versions of
libraries. Yet there are compatibility issues with this I encountered. Is
there any other way, such as somehow bringing newer dependent libraries into
anaconda as part of the package installation? Does it make sense at all?
I hope someone can help resolve this and that there is a resolution.
Jacob
Sent from my iPhone
On Jul 10, 2014, at 10:11 AM, Filipe Pires Alvarenga Fernandes

Post by Trent Nelson
Just to further what Ilan said, I would expect to see this if I conda
built on a newer version of Linux (with a later glibc), then tried to run
that binary on an older version.
I think wakari is centos 6.x.
We build all our official anaconda packages on centos 5 to avoid this.
@Sean: what version of Linux do the binstar builders run? Richard: you
could try building via binstar.

Hi Trent,
I am having the same issue. I was using conda build inside my wakari shell
as a work around to that problem, but you mentioned building it via
binstar. Can you point me to the docs on how to do that?
Thanks,
-Filipe

Post by Trent Nelson
Sent from my iPhone
It looks like the C++ runtime library on the Wakari system is incompatible
with the build of Iris. Which system is Wakari running on? What is
/etc/issue.
Thanks Ilan

Post by Richard Signell
Conda folks,
We successfully built Iris as a conda module on Linux64 and have
conda install -c rsignell iris==1.7.0_dev_395c61d
but on Wakari (np18py27-1.9), although it installs, when I try to import
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not
found (required by
/opt/anaconda/envs/np18py27-1.9/lib/python2.7/site-packages/cartopy/trace.so)
Any idea how to fix this?
-Rich
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<WxPythonCondaBuild.zip>

[Work]

Hi Trent, Hi Aaron,

It seems that the GLIB issue was a distraction. The issue with WxPython was incompatibility issue between Windows and Linux with one of the commands that I changed when migrating to version 3.

Perhaps it is connected to some library or behavior. Yet I was able to find a fix that does not require building WxPython. The current version of WxPython conda installs by default works on CentOs7 after I applied the fix.

However, do note that this version does not work on Ubuntu and the version that Aaron has in his channel that does work on ubuntu still raises many deprecation warnings.

Trent, if you still have extra time and can resolve the GLIBC issue and build a conda install of wxpython that works on Ubuntu 12.04 and 14.04 it will be tested, and much appreciated.

Jacob

Sent from my iPhone

Post by Work
Hi Aaron,
Your suggestion to use CentOS seems to be progress. However, there are still incompatibilities with CentOs7.
The good news are that conda install wxpython works without raising warnings. However, there are still some funny behavior that is incompatible with the windows WxPython.
The bad news are that building WxPython on CentOs7 is far from trivial. Some dependent libraries are not the same as Ubuntu and after several attempts I stopped trying on a gstreamer error while building. I did not even get to the point where GLibC is the issue.
Another issue is that the CentOS 7 repo does not seem to have grid engine, which I need. Perhaps I should downgrade to an earlier version of CentOS. However, I already had things working at almost the same level with Ubuntu 12.04.
Perhaps the issues I am encountering of WxPython not being compatible with the windows behavior is a WxPython issue and the problem is solved for me on Ubuntu 12.04 LTS. Perhaps I should not try to build WxPython at all.
I will explore this option. So Trent, unless you have other reasons to resolve this issue for Ubuntu you may wish to delay trying to rebuild the WxPython conda package. Aaron and Travis did this already and even if you success it may not resolve my issue. I was assuming this is an OS incompatibility issue, yet I may be wrong and have to verify this.
I hope this message saves you some time.
Jacob
Sent from my iPhone

Post by Jacob Barhak
Thanks Trent,
Your offer is appreciated.
You will find attached a zip file with the build.sh and meta.yaml. the meta.yaml is a copy of what Travis and Aaron did and is available on binstar. build.sh is a bit different since WxPython 3.0 now has its own build script.
I have an Ubuntu VM where it builds yet does not run with the GLIBC issue.
sudo apt-get install mesa-common-dev libgl1-mesa-glx libglu1-mesa libgl1-mesa-dev libglu1-mesa-dev libgstreamer0.10-dev libgconf2-dev libsdl1.2-dev zlib1g-dev libjpeg62-dev python-gst0.10-dev libgtk2.0-dev
When I ran this, I created a condabuild directory under WxPython and launched conda build from there - yet may want to perform the modifications needed in the build command.
Finally. note that WxPython build does work on Ubuntu 14.04 without anaconda to the degree that the demo runs. So the issue is Ubuntu+Anaconda+WxPythonand specifically the libraries.
While you try to improve this, I will try building on CentOs7. Aaron recommended version 5, yet if version 7 is already out I and does not match this issue will have to gain priority if you want to support multiple Linux platforms for multiple packages.
I hope at least one stable solution can be found.
Jacob

Hey Jacob can you point us at the WxPython recipe you’ve got going so far?
I may be able to find some time to take a crack at it this week.

Post by Work
Hi Aaron,
Is there a possibility of a partial GLIB solution before you have a build service ready and running? Something at the level of guidelines on how to build a package for anaconda?
Specific to the issue I mentioned, I want my package to work with the same libraries anaconda 2.01 is delivered with. So when I compile it I wish to use the libraries anaconda uses after a fresh install. There should be a way to do this.
I will take Ubuntu 14.04 LTS as an example. Upon a fresh install and importing libraries needed to compile WxPython the libm.so.6 file points to libm-2.19.so while the anaconda install uses libm-2.5.so. I assume that since WxPython is compiled against the former and ran against the latter it results in the incompatibility issue.
Is there a way to tell the Package build process to use the anaconda libraries rather than the Linux default libraries? I want my code to run on the same anaconda version and same Linux version I built the library in. I was thinking of changing the libm.so.6 link to point to the anaconda library before the build, yet there should be a more elegant way. For example, is it possible to install the same libraries that anaconda uses on Linux so the libraries will match and then build the package. Is this more elegant? Will it work? If yes, what environment should I have to match anaconda? What Linux packages should I install?
If I understand, this is part of the build service environment you plan to offer, yet is there anything that can be done before such a service is available?
I hope there is a solution close at hand.
Jacob
Sent from my iPhone

Post by Aaron Meurer
There have been discussions on building a libc conda package, but it's
not clear if it will work, or how easy it will be to do.
Aaron Meurer

Post by Work
Hi Ilan Hi Trent,
The GLIBC issue seems to be a recurring issue in many packages.
Here is a link to a discussion I started on the WxPython group that has a
https://groups.google.com/forum/m/#!topic/wx-users/75mT1NpbbBo
From what I am reading, I understand that different Linux distributions
carry different libraries compiled differently. In other words, there are
multiple versions of code for Linux. Therefore there may be a need to allow
multiple Linux binaries built for multiple platforms. If I understand this
correctly, this can result in a ridiculous number of binary versions. Please
correct me if I am wrong.
One solution I saw quoted by people is building against older versions of
libraries. Yet there are compatibility issues with this I encountered. Is
there any other way, such as somehow bringing newer dependent libraries into
anaconda as part of the package installation? Does it make sense at all?
I hope someone can help resolve this and that there is a resolution.
Jacob
Sent from my iPhone
On Jul 10, 2014, at 10:11 AM, Filipe Pires Alvarenga Fernandes

Post by Trent Nelson
Just to further what Ilan said, I would expect to see this if I conda
built on a newer version of Linux (with a later glibc), then tried to run
that binary on an older version.
I think wakari is centos 6.x.
We build all our official anaconda packages on centos 5 to avoid this.
@Sean: what version of Linux do the binstar builders run? Richard: you
could try building via binstar.

Hi Trent,
I am having the same issue. I was using conda build inside my wakari shell
as a work around to that problem, but you mentioned building it via
binstar. Can you point me to the docs on how to do that?
Thanks,
-Filipe

Post by Trent Nelson
Sent from my iPhone
It looks like the C++ runtime library on the Wakari system is incompatible
with the build of Iris. Which system is Wakari running on? What is
/etc/issue.
Thanks Ilan

Post by Richard Signell
Conda folks,
We successfully built Iris as a conda module on Linux64 and have
conda install -c rsignell iris==1.7.0_dev_395c61d
but on Wakari (np18py27-1.9), although it installs, when I try to import
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not
found (required by
/opt/anaconda/envs/np18py27-1.9/lib/python2.7/site-packages/cartopy/trace.so)
Any idea how to fix this?
-Rich
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<WxPythonCondaBuild.zip>

[Yaser Sakkaf]

Hi,
I advice you that don't even try to install glibc. It will give you
segmentation fault each time you try to run python.
Find some other solution.

Post by Richard Signell
Conda folks,
conda install -c rsignell iris==1.7.0_dev_395c61d
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /opt/anaconda/envs/np18py27-1.9/lib/python2.7/site-packages/cartopy/trace.so)
Any idea how to fix this?
-Rich