[petsc-users] Error with file linking

[Wee-Beng TAY]

Hi Satish,

It finally worked!

Thank you very much and have a nice day!

Yours sincerely,

Wee-Beng Tay


On 13/5/2010 1:56 AM, Satish Balay wrote:
> try the attached makefile. If you have problems copy/paste the
> *complete* make session from your terminal.
>
> Satish
>
> On Thu, 13 May 2010, Wee-Beng TAY wrote:
>
>    
>> Hi Satish,
>>
>> I tried to run it, with the -c present and absent. However, nothing happened.
>> I run using "make". I also specified "export
>> PETSC_DIR=/home/svu/g0306332/codes/petsc-3.1-p0/" and "export
>> PETSC_ARCH=atlas5-mpi-nodebug" before that.
>>
>> Did I miss out something?
>>
>> Also supposed that I have the same flag for all sources. In that case, how can
>> I build them?
>>
>> Thank you very much and have a nice day!
>>
>> Yours sincerely,
>>
>> Wee-Beng Tay
>>
>>
>> On 13/5/2010 1:27 AM, Satish Balay wrote:
>>      
>>> Attaching the modified makefile. It might need a couple of iterations
>>> of fixing.
>>>
>>> Hopefully its clear why it would work. Note - if not for different
>>> flags required for different sources (opt/opt2/opt3) - you can build
>>> all petsc/non-petsc sources with petsc makefile targets.
>>>
>>>
>>>        
>>>> In my fortran files, do I simply use petsc.h or I have to use specific *.h
>>>> depending on what petsc commands are used?
>>>>
>>>>          
>>> With petsc-3.1 you just have to use petsc.h for all F77 interface stuff, and
>>> petsc.h90 for all f90 interface stuff [like VecGetArrayF90()]
>>>
>>> Satish
>>>
>>> On Thu, 13 May 2010, Wee-Beng TAY wrote:
>>>
>>>
>>>        
>>>> Hi Satish,
>>>>
>>>> Sorry for the confusion.
>>>>
>>>> I have attached my makefile. This was used to compile and link my code
>>>> before
>>>> I used PETSc 3.1.
>>>>
>>>> I have several fortran files. Some contain PETSc commands and need to use
>>>> PETSc include files. Other do not. In the end, they all have to be linked
>>>> to
>>>> form my final code. I used to copy part of the compiling and linking
>>>> command
>>>> from "make ex1f" to compile my code:
>>>>
>>>> /app1/mvapich2/current/bin/mpif90 -c  -O3
>>>> -I/home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/include
>>>> -I/home/svu/g0306332/codes/petsc-3.1-p0/include
>>>> -I/home/svu/g0306332/lib/hypre-2.6.0b_atlas5/include
>>>> -I/app1/mvapich2/1.4/include -I/app1/mvapich2/current/include
>>>> -I/home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/include
>>>> -I/home/svu/g0306332/lib/hypre-2.6.0b_atlas5/include
>>>> -I/app1/mvapich2/1.4/include -I/app1/mvapich2/current/include    -o ex1f.o
>>>> ex1f.F
>>>>
>>>> /app1/mvapich2/current/bin/mpif90 -O3   -o ex1f ex1f.o
>>>> -Wl,-rpath,/home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib
>>>> -L/home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib -lpetsc
>>>> -Wl,-rpath,/home/svu/g0306332/lib/hypre-2.6.0b_atlas5/lib
>>>> -L/home/svu/g0306332/lib/hypre-2.6.0b_atlas5/lib -lHYPRE -lmpichcxx
>>>> -lstdc++
>>>> -Wl,-rpath,/app1/intel/mkl/10.0.5.025/lib/em64t
>>>> -L/app1/intel/mkl/10.0.5.025/lib/em64t -lmkl_lapack -lmkl -lguide
>>>> -lpthread
>>>> -L/app1/mvapich2/1.4/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -ldl
>>>> -lmpich
>>>> -lpthread -lrdmacm -libverbs -libumad -lrt -lgcc_s -lmpichf90
>>>> -L/app1/intel/Compiler/11.0/074/lib/intel64 -lifport -lifcore -limf -lsvml
>>>> -lm
>>>> -lipgo -lirc -lirc_s -lm -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl
>>>> -lmpich
>>>> -lpthread -lrdmacm -libverbs -libumad -lrt -lgcc_s -ldl
>>>>
>>>> However, it doesn't seem to work now. I tried to look at chapter 14 but I
>>>> don't really understand since I know very little about makefiles.
>>>>
>>>> Can you give a rough guide for my case? I will try to read up on the
>>>> manual to
>>>> get more info.
>>>>
>>>> Moreover, I am confused by the use of:
>>>>
>>>> #include "finclude/petsc.h" etc.
>>>>
>>>> In my fortran files, do I simply use petsc.h or I have to use specific *.h
>>>> depending on what petsc commands are used?
>>>>
>>>> Thank you very much and have a nice day!
>>>>
>>>> Yours sincerely,
>>>>
>>>> Wee-Beng Tay
>>>>
>>>>
>>>> On 12/5/2010 9:55 AM, Satish Balay wrote:
>>>>
>>>>          
>>>>> Lets step back and deal with this primary issue.
>>>>>
>>>>> Have you attempted to use makefiles in petsc format? What problems
>>>>> have you encountered? Perhaps they are fixable.
>>>>>
>>>>> The reason to use this format is to make your makefile as portable as
>>>>> possible [and avoid such issues].
>>>>>
>>>>> Satish
>>>>>
>>>>> On Tue, 11 May 2010, Satish Balay wrote:
>>>>>
>>>>>
>>>>>
>>>>>            
>>>>>> Why not use petsc makefiles - and avoid these hasseles?
>>>>>>
>>>>>>
>>>>>>
>>>>>>              
>>>>>
>>>>>