liblsf.so: undefined symbol: shm_open #12
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What version of LSF? |
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@adamsla We are using LSF 10.1. Is LSF DRMAA supporting LSF 10.1 ? If not, then it would be cool if IBM could make a new DRMAA release that supports version 10.1 as I would like to recommend to our cluster users to use DRMAA to interface with the LSF batch scheduler instead of using any third-party software. I tried to recompile LSF DRMAA 1.1.1 with LSF 10.1 but already the configure script is failing. Please find below an excerpt from the config.log: |
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Samual, These are compile time options. I encountered the same issue while playing with this on the latest version of LSF too. We need to change the compatibility level in the configure scripts. Though I did see this, I did not ever get to the point of updating the configure.ac to incorporate the required compatibility level. It's a simple thing. If you google for this, you should be able to find the specific flags to change/remove. The way we are doing support on this and the other packages housed here at this site, is to be primarily community driven. So, if you find the options, simply create a pull request with the required Sign Off section, and we will merge the update strait away. If you don't feel comfortable with that, let us know. I can ask a Dev to take some time to perform that change, though it'll take a few days. Simply let us know. Larry |
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@adamsla: I would not feel comfortable doing a PR myself and would be happy if you could ask a dev to fix this problem. I did some investigation on this problem a found a few things that I would like to share with you. In LSF 9.1.2, the header file lsbatch.h did not have any C++ style single line comments. Single line comments were done like /* this is a comment */ instead of // this is a comment When looking at lsbatch.h in LSF 10.1, around line 3486, there were four lines with C++ single line comments added (//) This is not compatible with the -ansi compiler option of gcc and therefore breaks LSF DRMAA (at line 11546 in configure and at line 70 in configure.ac, you set the -ansi option). The GCC manpage states:
Therefore the configure script of LSF DRMAA fails. |
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Yea, if memory serves me well, we should be removing the |
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@samfux84, what is your build environment? What OS and version? |
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We solved this by adding As a workaround to the |
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Both good suggestions. I'll do a commit to correct as soon as I have a few cycles. |
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@adamsla Please find below information about my build environment: OS: CentOS Linux release 7.4.1708 (Core) @jakirkham Thank you for providing these hints. I will try to build LSF DRMAA 1.1.1 with these hints. |
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I tried again to compile LSF DRMAA, this time of our second cluster (CentOS Linux release 7.5, GCC 4.8.5, LSF verison 10.1). Even when following all hints from this issue, it is still not compiling. Can you please provide a release that is not broken ? I have a request from a user of our cluster that requires this library for his workflow to run on the cluster, as the software that he would like to use depends on LSF DRMAA to submit jobs to the cluster. Any help is appreciated. Please find below the entire logs: |
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First thing that I tried was to run autoreconf -i --force to get the missing scripts. This then cause even more errors: |
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Release 1.1.1 seems to be fundamentally broken. But when switching to the master branch, it compiles using the hints proposed in this ticket. Can you please make a new release using the current master branch ? Best regards Sam |
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I have installed the python-drmaa bindings for LSF DRMAA 1.1.1 and when I try to import the package, it fails with the following error message:
Is this a known problem ? And can you provide any help with this issue ?
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