libboost_iostreams.so.1.61.0: cannot open shared object file: No such file or directory
I am using Anaconda as my main python distribution (though also have the system's default python installed) so have to compile graph-tool from source to get it to work with Anaconda. I am using Ubuntu 14.04 so also have to compile boost from source to be able to use the full functionality of graph-tool. I have done so and they have both installed without any error messages, however, when then importing graph-tool in python using `from graph_tool.all import *` I get the error message `ImportError: libboost_iostreams.so.1.61.0: cannot open shared object file: No such file or directory`. How could I go about solving that problem/what is this caused by? Best wishes, Philipp -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
Do you have libboost_iostreams.so.1.61.0 in your anaconda/lib folder? On Wed, Jun 22, 2016 at 11:36 AM, P-M [via Main discussion list for the graph-tool project] <ml-node+s982480n4026599h93@n3.nabble.com> wrote:
I am using Anaconda as my main python distribution (though also have the system's default python installed) so have to compile graph-tool from source to get it to work with Anaconda. I am using Ubuntu 14.04 so also have to compile boost from source to be able to use the full functionality of graph-tool. I have done so and they have both installed without any error messages, however, when then importing graph-tool in python using `from graph_tool.all import *` I get the error message `ImportError: libboost_iostreams.so.1.61.0: cannot open shared object file: No such file or directory`.
How could I go about solving that problem/what is this caused by?
Best wishes,
Philipp
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No, that file is in "/home/pmj27/software/boost_1_61_0/stage/lib". anaconda/lib contains "libboost_iostreams.so.1.58.0" and "libboost_iostreams.so". -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
Having done some re-installing the problem still persists. The file in question is in the folder "/home/pmj27/software/boost_1.61/lib". During ./configure I did however provide that path as LDFLAGS="-L/home/pmj27/software/boost_1.61/lib". Does anybody know where I am going wrong? -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
On 24.06.2016 20:23, P-M wrote:
Having done some re-installing the problem still persists. The file in question is in the folder "/home/pmj27/software/boost_1.61/lib". During ./configure I did however provide that path as LDFLAGS="-L/home/pmj27/software/boost_1.61/lib". Does anybody know where I am going wrong?
Is the above path also in your LD_LIBRARY_PATH? Otherwise the linker will not find it. Best, Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>
How would I check this/how would I add it? I haven't added it manually so this may be the cause. Best, Philipp From: Tiago Peixoto [via Main discussion list for the graph-tool project] [mailto:ml-node+s982480n4026612h70@n3.nabble.com] Sent: 28 June 2016 07:32 To: P-M <pmj27@cam.ac.uk> Subject: Re: libboost_iostreams.so.1.61.0: cannot open shared object file: No such file or directory On 24.06.2016 20:23, P-M wrote:
Having done some re-installing the problem still persists. The file in question is in the folder "/home/pmj27/software/boost_1.61/lib". During ./configure I did however provide that path as LDFLAGS="-L/home/pmj27/software/boost_1.61/lib". Does anybody know where I am going wrong?
Is the above path also in your LD_LIBRARY_PATH? Otherwise the linker will not find it. Best, Tiago -- Tiago de Paula Peixoto <[hidden email]> _______________________________________________ graph-tool mailing list [hidden email] https://lists.skewed.de/mailman/listinfo/graph-tool <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com /images/icon_attachment.gif> signature.asc (836 bytes) Download Attachment <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com /attachment/4026612/0/signature.asc> -- Tiago de Paula Peixoto <tiago@skewed.de <mailto:tiago@skewed.de> > _____ If you reply to this email, your message will be added to the discussion below: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/ libboost-iostreams-so-1-61-0-cannot-open-shared-object-file-No-such-file-or- directory-tp4026599p4026612.html To unsubscribe from libboost_iostreams.so.1.61.0: cannot open shared object file: No such file or directory, click here <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com /template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4026599&code=cG1qMj dAY2FtLmFjLnVrfDQwMjY1OTl8OTE3MzUzNDc5> . <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com /template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemai l.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.N abbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_sub scribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_ins tant_email%21nabble%3Aemail.naml> NAML -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
On 28.06.2016 13:46, P-M wrote:
How would I check this/how would I add it? I haven’t added it manually so this may be the cause…
It is an environment variable. You check it with echo $LD_LIBRARY_PATH and you set it with export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/pmj27/software/boost_1.61/lib -- Tiago de Paula Peixoto <tiago@skewed.de>
I have done that. It didn’t work though. I have set the path in .bashrc too so typing echo $LD_LIBRARY_PATH returns /home/pmj27/software/boost_1.61/lib but the problem still persists unfortunately. Best wishes, Philipp From: Tiago Peixoto [via Main discussion list for the graph-tool project] [mailto:ml-node+s982480n4026622h80@n3.nabble.com] Sent: 28 June 2016 13:52 To: P-M <pmj27@cam.ac.uk> Subject: Re: libboost_iostreams.so.1.61.0: cannot open shared object file: No such file or directory On 28.06.2016 13:46, P-M wrote:
How would I check this/how would I add it? I haven’t added it manually so this may be the cause…
It is an environment variable. You check it with echo $LD_LIBRARY_PATH and you set it with export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/pmj27/software/boost_1.61/lib -- Tiago de Paula Peixoto <[hidden email]> _______________________________________________ graph-tool mailing list [hidden email] https://lists.skewed.de/mailman/listinfo/graph-tool <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/images/icon_attachment.gif> signature.asc (836 bytes) Download Attachment <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/attachment/4026622/0/signature.asc> -- Tiago de Paula Peixoto <tiago@skewed.de <mailto:tiago@skewed.de> > _____ If you reply to this email, your message will be added to the discussion below: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... To unsubscribe from libboost_iostreams.so.1.61.0: cannot open shared object file: No such file or directory, click here <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4026599&code=cG1qMjdAY2FtLmFjLnVrfDQwMjY1OTl8OTE3MzUzNDc5> . <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> NAML -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
On 29.06.2016 14:41, P-M wrote:
I have done that. It didn’t work though. I have set the path in .bashrc too so typing echo $LD_LIBRARY_PATH returns /home/pmj27/software/boost_1.61/lib but the problem still persists unfortunately.
This is all very simple, if it can't find the library object file, it must be because the path is wrong. In a previous email, you said the library file was in: /home/pmj27/software/boost_1_61_0/stage/lib, which is different from the above. Just find the correct directory where the library is and it must work. -- Tiago de Paula Peixoto <tiago@skewed.de>
I have re-installed boost since that email. Typing “sudo find $HOME -name 'libboost_iostreams.so.1.61.0'” into the terminal returns: /home/pmj27/software/boost_1.61/bin.v2/libs/iostreams/build/gcc-5.3.0/release/threading-multi/libboost_iostreams.so.1.61.0 /home/pmj27/software/boost_1.61/lib/libboost_iostreams.so.1.61.0 So it definitely exists in “/home/pmj27/software/boost_1.61/lib” but isn’t being picked up. Best, Philipp From: Tiago Peixoto [via Main discussion list for the graph-tool project] [mailto:ml-node+s982480n4026627h35@n3.nabble.com] Sent: 29 June 2016 13:46 To: P-M <pmj27@cam.ac.uk> Subject: Re: libboost_iostreams.so.1.61.0: cannot open shared object file: No such file or directory On 29.06.2016 14:41, P-M wrote:
I have done that. It didn’t work though. I have set the path in .bashrc too so typing echo $LD_LIBRARY_PATH returns /home/pmj27/software/boost_1.61/lib but the problem still persists unfortunately.
This is all very simple, if it can't find the library object file, it must be because the path is wrong. In a previous email, you said the library file was in: /home/pmj27/software/boost_1_61_0/stage/lib, which is different from the above. Just find the correct directory where the library is and it must work. -- Tiago de Paula Peixoto <[hidden email]> _______________________________________________ graph-tool mailing list [hidden email] https://lists.skewed.de/mailman/listinfo/graph-tool <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/images/icon_attachment.gif> signature.asc (836 bytes) Download Attachment <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/attachment/4026627/0/signature.asc> -- Tiago de Paula Peixoto <tiago@skewed.de <mailto:tiago@skewed.de> > _____ If you reply to this email, your message will be added to the discussion below: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... To unsubscribe from libboost_iostreams.so.1.61.0: cannot open shared object file: No such file or directory, click here <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4026599&code=cG1qMjdAY2FtLmFjLnVrfDQwMjY1OTl8OTE3MzUzNDc5> . <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> NAML -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
On 29.06.2016 14:52, P-M wrote:
So it definitely exists in “/home/pmj27/software/boost_1.61/lib” but isn’t being picked up.
As I see it, there are two options: (a) either your system is broken at a fundamental level or (b) there is an inconsistency with your paths. I think (b) is more likely. Another possibility is that anaconda is somehow interfering with the loader... -- Tiago de Paula Peixoto <tiago@skewed.de>
Thank you for the help so far! I’m not sure my expertise is great enough to debug this so I have deleted that installation of graph-tool and instead set up a virtual environment where I have linked to the apt-get version of graphtool (http://damcb.com/setting-up-a-scientific-python-working-environment.html ). That seems to import (mostly) fine. Best, Philipp From: Tiago Peixoto [via Main discussion list for the graph-tool project] [mailto:ml-node+s982480n4026629h97@n3.nabble.com] Sent: 29 June 2016 14:14 To: P-M <pmj27@cam.ac.uk> Subject: Re: libboost_iostreams.so.1.61.0: cannot open shared object file: No such file or directory On 29.06.2016 14:52, P-M wrote:
So it definitely exists in “/home/pmj27/software/boost_1.61/lib” but isn’t being picked up.
As I see it, there are two options: (a) either your system is broken at a fundamental level or (b) there is an inconsistency with your paths. I think (b) is more likely. Another possibility is that anaconda is somehow interfering with the loader... -- Tiago de Paula Peixoto <[hidden email]> _______________________________________________ graph-tool mailing list [hidden email] https://lists.skewed.de/mailman/listinfo/graph-tool <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/images/icon_attachment.gif> signature.asc (836 bytes) Download Attachment <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/attachment/4026629/0/signature.asc> -- Tiago de Paula Peixoto <tiago@skewed.de <mailto:tiago@skewed.de> > _____ If you reply to this email, your message will be added to the discussion below: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... To unsubscribe from libboost_iostreams.so.1.61.0: cannot open shared object file: No such file or directory, click here <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4026599&code=cG1qMjdAY2FtLmFjLnVrfDQwMjY1OTl8OTE3MzUzNDc5> . <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> NAML -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
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Tiago de Paula Peixoto