[FLASH-USERS] FLASH make error

Fri Nov 15 17:26:09 EST 2024

Hi Peter,

Based on the link error it might be the case that your hdf5 is not built with “-parallel”, given that all the symbols it’s complaining about are mpi related. You can check your include directory for the “H5_HAVE_PARALLEL” macro, for example I get

> (base) ➜  include pwd    
> /usr/local/gnu-14/hdf5/include
> (base) ➜  include grep -i h5_have_parallel H5pubconf.h
> #define H5_HAVE_PARALLEL 1
> #define H5_HAVE_PARALLEL_FILTERED_WRITES 1
*********************************************
Adam Reyes

Code Group Leader, Flash Center for Computational Science  
Research Scientist, Dept. of Physics and Astronomy
University of Rochester
River Campus: Bausch and Lomb Hall, 369  
500 Wilson Blvd. PO Box 270171, Rochester, NY 14627
Email adam.reyes at rochester.edu
Web https://flash.rochester.edu
 (he / him / his)

*********************************************

> On Nov 15, 2024, at 9:05 AM, Peter Manzella <peter.manzella at maine.edu> wrote:
> 
> Ryan,
> 
> That was helpful. I was able to use both your screenshots and advice to fix some things ( I think). I have double and triple checked my paths, with no progress at all. I do not know where else to look, any advice on how to proceed would be greatly appreciated (I did not know that the switch made on the cluster since when I last had this working would prevent me from using FLASH in this manner).
> 
> On Thu, Nov 14, 2024 at 10:29 PM Ryan Farber <rjfarber at umich.edu <mailto:rjfarber at umich.edu>> wrote:
>> Hi Peter,
>> 
>> Thanks for the screenshot and your Makefile.h. To echo what Klaus wrote in the FLASH mailing list post you linked to, your Makefile.h has problems.
>> 
>> The error you’re receiving is in the linking step and is complaining about hdf5 and/or MPI files not being found.
>> 
>> I noticed that you have LIB_NCMPI set (for netcdf) as well as CFLAGS_NCMPI.
>> 
>> You should instead set the corresponding MPI variables.
>> 
>> Also note that you have -ggdb in your *_OPT variables, which is very useful for debugging but not ideal for production runs. I’d also recommend -O3, unless you’re worried about one or more of its optimizations being inappropriate for your system.
>> 
>> Probably the above should be enough, but I’ve attached screenshots (on my phone so they might not be the easiest to parse) in case they help.
>> 
>> You might also need to check that your paths exist and update the paths you set in Makefile.h as needed.
>> 
>> Best wishes,
>> Ryan<image0.png><image1.png><image2.png><image3.png><image4.png>
>> 
>> Sent from my iPhone
>> 
>>> On 14. Nov 2024, at 17:33, Peter Manzella <peter.manzella at maine.edu <mailto:peter.manzella at maine.edu>> wrote:
>>> 
>>> 
>>> Ryan,
>>> 
>>> My apologies, I was in a rush, and forgot the screenshot as well. This is the error I get at the very end of running make,
>>> <image.png>
>>> 
>>> In case it is helpful, attached is my Makefile.h, and here is the setup command:
>>> ./setup CCSN -auto -2d +cylindrical -nxb=16 -nyb=16 -objdir ccsn2d threadBlockList=False +pm4dev threadWithinBlock=False +newMpole +uhd +hdf5TypeIO useFortran2003=True
>>> 
>>> On Thu, Nov 14, 2024 at 6:30 PM Ryan Farber <rjfarber at umich.edu <mailto:rjfarber at umich.edu>> wrote:
>>>> Hi Peter,
>>>> 
>>>> It would be helpful if you can explain what issue you encountered (screenshots welcomed).
>>>> 
>>>> Best wishes,
>>>> Ryan
>>>> 
>>>> Sent from my iPhone
>>>> 
>>>>> On 14. Nov 2024, at 14:05, Peter Manzella <peter.manzella at maine.edu <mailto:peter.manzella at maine.edu>> wrote:
>>>>> 
>>>>> 
>>>>> I actually did not know that I could use google to search the mailing list, that is helpful. I resolved that issue, but a new one has come up, that after checking the mailing list, I still am unsure. I found this thread, https://flash.rochester.edu/pipermail/flash-users/2016-June/006310.html , but as I had mentioned before, I'm pretty sure my Makefile.h is good, so I am not sure where to look now. I had FLASH working but the cluster admin must have changed some things around and FLASH no longer works properly.
>>>>> 
>>>>> On Thu, Nov 14, 2024 at 3:55 PM Ryan Farber <rjfarber at umich.edu <mailto:rjfarber at umich.edu>> wrote:
>>>>>> Hi Peter,
>>>>>> 
>>>>>> I’m not in front of my computer now but this is another very common issue. If you google search the flash mailing list you should find the solution to your compilation error quite readily.
>>>>>> 
>>>>>> Best wishes,
>>>>>> Ryan
>>>>>> 
>>>>>> Sent from my iPhone
>>>>>> 
>>>>>>> On 14. Nov 2024, at 10:10, Peter Manzella <peter.manzella at maine.edu <mailto:peter.manzella at maine.edu>> wrote:
>>>>>>> 
>>>>>>> 
>>>>>>> Ryan,
>>>>>>> 
>>>>>>> Thank you very much! That worked, I have another error now, but I think it may have to do with the version of the links in makefile.h,
>>>>>>> <image.png>
>>>>>>> 
>>>>>>> If that is the case, I have no way of getting back to a different version as I have been unable to contact the cluster admin for assistance. Help is again very much appreciated.
>>>>>>> 
>>>>>>> On Thu, Nov 14, 2024 at 11:24 AM Ryan Farber <rjfarber at umich.edu <mailto:rjfarber at umich.edu>> wrote:
>>>>>>>> Hi Peter,
>>>>>>>> 
>>>>>>>> Comment out the section of your Makefile.h (mine was at the bottom) that has iso_c_binding
>>>>>>>> https://flash.rochester.edu/pipermail/flash-users/2024-May/008664.html
>>>>>>>> 
>>>>>>>> Best wishes,
>>>>>>>> --------
>>>>>>>> Ryan
>>>>>>>> 
>>>>>>>> 
>>>>>>>> On Thu, Nov 14, 2024 at 6:53 AM Peter Manzella <peter.manzella at maine.edu <mailto:peter.manzella at maine.edu>> wrote:
>>>>>>>>> Hello,
>>>>>>>>> 
>>>>>>>>> I am trying to get FLASH running on my university cluster after they moved user interfaces and now it is no longer working, I can setup the problem, but when I run 'make' I encounter this error,
>>>>>>>>> <image.png>
>>>>>>>>> 
>>>>>>>>> I am pretty sure the makefile.h is accurate, is there a way to check that? Or are there other ways to check how to fix this? Thanks!
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> -- 
>>>>>>>>> Peter Manzella
>>>>>>>>> PhD Candidate, Department of Physics and Astronomy
>>>>>>>>> 309 Bennett Hall
>>>>>>>>> University of Maine
>>>>>>>>> peter.manzella at maine.edu <mailto:peter.manzella at maine.edu>
>>>>>>>>> 
>>>>>>>>> “If you run out of ideas follow the road; you'll get there.” – Edgar Allan Poe
>>>>>>>>> _______________________________________________
>>>>>>>>> flash-users mailing list
>>>>>>>>> flash-users at flash.rochester.edu <mailto:flash-users at flash.rochester.edu>
>>>>>>>>> 
>>>>>>>>> For list info, including unsubscribe:
>>>>>>>>> https://flash.rochester.edu/mailman/listinfo/flash-users
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> -- 
>>>>>>> Peter Manzella
>>>>>>> PhD Candidate, Department of Physics and Astronomy
>>>>>>> 309 Bennett Hall
>>>>>>> University of Maine
>>>>>>> peter.manzella at maine.edu <mailto:peter.manzella at maine.edu>
>>>>>>> 
>>>>>>> “If you run out of ideas follow the road; you'll get there.” – Edgar Allan Poe
>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
>>>>> Peter Manzella
>>>>> PhD Candidate, Department of Physics and Astronomy
>>>>> 309 Bennett Hall
>>>>> University of Maine
>>>>> peter.manzella at maine.edu <mailto:peter.manzella at maine.edu>
>>>>> 
>>>>> “If you run out of ideas follow the road; you'll get there.” – Edgar Allan Poe
>>> 
>>> 
>>> 
>>> -- 
>>> Peter Manzella
>>> PhD Candidate, Department of Physics and Astronomy
>>> 309 Bennett Hall
>>> University of Maine
>>> peter.manzella at maine.edu <mailto:peter.manzella at maine.edu>
>>> 
>>> “If you run out of ideas follow the road; you'll get there.” – Edgar Allan Poe
>>> <Makefile.h>
> 
> 
> 
> -- 
> Peter Manzella
> PhD Candidate, Department of Physics and Astronomy
> 309 Bennett Hall
> University of Maine
> peter.manzella at maine.edu <mailto:peter.manzella at maine.edu>
> 
> “If you run out of ideas follow the road; you'll get there.” – Edgar Allan Poe
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> 
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