[Users] ET_2014_05 fails to build on Linux Mint 17
Dumsani Ndzinisa
g14n8326 at campus.ru.ac.za
Thu Jun 26 10:11:32 CDT 2014
Hi Ian,
Ah I'm sorry I didn't realize that my replying wasn't directed to
the group. I guess this all has to do with me being very on
almost everything here! I will append my previous response
here.
Many thanks to you!!! Commenting out hwloc from the thornlist
has done the trick. My ET has compiled successfully now. Being
the newbie that I am, please do expect me to get back again and
bother you will plenty of elementary questions.
Thanks again.
My previous response which was communicated off the group...here.......
> Hi Ian,
>
> Yes, I do have a local installation of the hwloc library. And I think
> you've really hit the
> nail on the head in your diagnosis. When I went through the make file,
> and also looked
> at the error message my understanding was that Cactus is trying to
> bring in numa
> when linking, and it looks for it in the wrong place. Running the command
> dpkg --get-selections | grep hwloc, this is the output I get:
> hwloc-nox install
> libhwloc-dev:amd64 install
> libhwloc5:amd64 install
>
> I'll implement the suggestions you gave to me, try to build again and
> get back here
> with some feedback.
On 26/06/2014 12:53, Ian Hinder wrote:
>
> On 26 Jun 2014, at 12:51, Dumsani Ndzinisa <g14n8326 at campus.ru.ac.za
> <mailto:g14n8326 at campus.ru.ac.za>> wrote:
>
>> Hi Ian,
>>
>> Yes, I do have a local installation of the hwloc library. And I think
>> you've really hit the
>> nail on the head in your diagnosis. When I went through the make
>> file, and also looked
>> at the error message my understanding was that Cactus is trying to
>> bring in numa
>> when linking, and it looks for it in the wrong place. Running the command
>> dpkg --get-selections | grep hwloc, this is the output I get:
>> hwloc-nox install
>> libhwloc-dev:amd64 install
>> libhwloc5:amd64 install
>>
>> I'll implement the suggestions you gave to me, try to build again and
>> get back here
>> with some feedback.
>
> Hi Dumsani,
>
> Glad to be of help! By the way, you replied just to me, not to the
> mailing list.
>
>>
>>
>> On 26/06/2014 12:22, Ian Hinder wrote:
>>> On 26 Jun 2014, at 11:56, Dumsani Ndzinisa <g14n8326 at campus.ru.ac.za
>>> <mailto:g14n8326 at campus.ru.ac.za>> wrote:
>>>
>>>> Hi everyone,
>>>>
>>>> I have a fresh checkout of the latest stable release of the
>>>> Einstein Toolkit
>>>> (ET_2014_05) which I'm trying to build on my laptop. The laptop is
>>>> running on Linux Mint 17, and I have adapted configuration options from
>>>> the bundled "ubuntu.cfg" file. On my machine, I have gcc version 4.8.2,
>>>> g++ version 4.8.2, and gfortran 4.8.2 as well.
>>>>
>>>> However, when building the toolkit (using the thornlist
>>>> "einsteintoolkit.th <http://einsteintoolkit.th>)
>>>> the build always fails no matter what I try. For instance, on my
>>>> very first
>>>> attempt, I didn't use any of my locally installed libraries but opted
>>>> for the
>>>> ones bundled with the toolkit. There was one error message in that case
>>>> pointing to the PAPI library having failed to get configured. I
>>>> then decided
>>>> to comment out this thorn from the thornlist (in the .th file).
>>>> From there
>>>> on, still building with the bundled external libraries, I have been
>>>> persistently
>>>> getting an error message (in the linking stage) to the effect a certain
>>>> library (lnuma) could not be found. Below is the error message that
>>>> gets
>>>> returned onto the screen:
>>>>
>>>> /usr/bin/ld: cannot find -lnuma
>>>> collect2: error: ld returned 1 exit status
>>>> /home/dumsani/Cactus/lib/make/make.configuration:147: recipe for target
>>>> '/home/dumsani/Cactus/exe/cactus_test-ET6' failed
>>>> make[1]: *** [/home/dumsani/Cactus/exe/cactus_test-ET6] Error 1
>>>> Makefile:254: recipe for target 'test-ET6' failed
>>>> make: *** [test-ET6] Error 2
>>>>
>>>> I would appreciate if anyone with some idea came to my rescue here.
>>>> Cactus and the ET are still very new to me. I've been stuck on this for
>>>> almost a week now. And I am of the idea that it shouldn't be taking me
>>>> that long. Together with my advisor, we have made a checkout of Cactus
>>>> (Llama thornlist) earlier and he did oriente me to the process until we
>>>> had a successful build (we got the executable) for the llama
>>>> thornlist. So,
>>>> now the idea is for me to get some more practice with Cactus/ET by
>>>> checking out the full toolkit, configuring, building and then
>>>> running some
>>>> example simulations provided in the toolkit.
>>> Hi,
>>>
>>> Can you try commenting out the thorn "hwloc" from your thornlist?
>>> Grepping through the source for "numa", the only use of this
>>> library seems to be hwloc. hwloc is a thorn which assists in
>>> binding software threads to physical computational cores and
>>> processes to processor sockets for efficiency, but it is not
>>> necessary for the toolkit to run.
>>>
>>> There might be something wrong with the hwloc configure script
>>> (Cactus/arrangements/ExternalLibraries/hwloc/configure.sh). The
>>> relevant lines appear to be
>>>
>>>> # Add libnuma manually, if necessary
>>>> if grep -q '[-]lnuma' ${HWLOC_LIB_DIR}/libhwloc.la 2>/dev/null; then
>>>> if ! echo '' ${HWLOC_LIBS} '' | grep -q ' numa '; then
>>>> HWLOC_LIBS="${HWLOC_LIBS} numa"
>>>> fi
>>>> fi
>>> This seems to be attempting to add the numa library to the link line
>>> if it is found in libhwloc.la. The error message indicates that
>>> numa has been added to the link line, but the library is not
>>> available on the link path.
>>>
>>> The most recent change to hwloc, in April (i.e. before the release), is:
>>>
>>> "Correct detecting whether -lnuma is necessary"
>>> (http://git.barrywardell.net/?p=arrangements/ExternalLibraries/hwloc.git;a=commitdiff;h=4a3b694661f69df842c12a1e188e42f546dd92e2)
>>> authoreschnett <eschnett at 152c557c-6d84-4bc7-9b1a-dfca721279c7>
>>> Sat, 19 Apr 2014 23:07:32 +0200 (21:07 +0000)
>>> committereschnett <eschnett at 152c557c-6d84-4bc7-9b1a-dfca721279c7>
>>> Sat, 19 Apr 2014 23:07:32 +0200 (21:07 +0000)
>>>
>>> Probably Erik has some insight into this.
>>>
>>> We have an automated build and test process running under Ubuntu
>>> 12.04, and this is working fine. It also builds hwloc from source,
>>> rather than relying on the Ubuntu version. Do you happen to have
>>> hwloc installed? Maybe it is conflicting with the self-built version?
>>>
>>> dpkg -l hwloc
>>>
>>> We should probably upgrade the build and test system to Ubuntu
>>> 14.04, as that is now the latest stable release. Maybe something in
>>> Ubuntu has changed with the hwloc library.
>>>
>>
>
> --
> Ian Hinder
> http://numrel.aei.mpg.de/people/hinder
>
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