Building Dalton on Fedora 24

[Henrique]

Dear colleagues, how are you?
I'm trying to build the latest Dalton code on my Fedora 24 but at the end of the compilation I'm getting this messages:

Code: Select all

[100%] Linking Fortran static library lib/libdalton.a
[100%] Built target dalton
Scanning dependencies of target dalton.x
[100%] Building Fortran object CMakeFiles/dalton.x.dir/DALTON/abacus/dalton.F.o
[100%] Linking Fortran executable dalton.x
lib/libdalton.a(ccsd_energy.F.o): In function `ishurwitz_':
ccsd_energy.F:(.text+0x70b): undefined reference to `dgeev_'
lib/libdalton.a(cc_lanczos_drv.F.o): In function `cc_lanczos_drv_':
cc_lanczos_drv.F:(.text+0x34cc): undefined reference to `dgeev_'
lib/libdalton.a(rspzfs.F.o): In function `zfsan1_':
rspzfs.F:(.text+0x1b6f): undefined reference to `zheev_'
rspzfs.F:(.text+0x2068): undefined reference to `dsyev_'
lib/libdalton.a(sirlocsel.F.o): In function `locsum_':
sirlocsel.F:(.text+0x1661): undefined reference to `dsyev_'
lib/libdalton.a(sirlocsel.F.o): In function `mexp_':
sirlocsel.F:(.text+0x201b): undefined reference to `zheev_'
lib/libdalton.a(sirqmmm.F.o): In function `make_qmmm_inverse_response_matrix_':
sirqmmm.F:(.text+0xf0fd): undefined reference to `dsptrf_'
sirqmmm.F:(.text+0xf6a0): undefined reference to `dsptri_'
lib/libdalton.a(sirqmmm.F.o): In function `get_ind_dipoles_1_':
sirqmmm.F:(.text+0x12c14): undefined reference to `dsptrf_'
sirqmmm.F:(.text+0x12c4e): undefined reference to `dsptri_'
lib/libdalton.a(sirstex.F.o): In function `matfun_':
sirstex.F:(.text+0x3b9): undefined reference to `dsyev_'
lib/libdalton.a(sirstex.F.o): In function `uaug_':
sirstex.F:(.text+0x8cd1): undefined reference to `dsyev_'
lib/libdalton.a(absorp.F.o): In function `absreduc_':
absorp.F:(.text+0xcafe): undefined reference to `zsysv_'
external/lib/libqfitlib.a(linear_solver.F90.o): In function `__linear_solver_MOD_linear_solve_svd':
linear_solver.F90:(.text+0x81f): undefined reference to `dgesvd_'
linear_solver.F90:(.text+0x95f): undefined reference to `dgesvd_'
external/lib/libpelib.a(pe_lapack_interfaces.f90.o): In function `__pe_lapack_interfaces_MOD_lansp':
pe_lapack_interfaces.f90:(.text+0xc7): undefined reference to `dlansp_'
external/lib/libpelib.a(pe_lapack_interfaces.f90.o): In function `__pe_lapack_interfaces_MOD_ppcon':
pe_lapack_interfaces.f90:(.text+0x241): undefined reference to `dppcon_'
external/lib/libpelib.a(pe_lapack_interfaces.f90.o): In function `__pe_lapack_interfaces_MOD_spcon':
pe_lapack_interfaces.f90:(.text+0x41d): undefined reference to `dspcon_'
external/lib/libpelib.a(pe_lapack_interfaces.f90.o): In function `__pe_lapack_interfaces_MOD_pptrs':
pe_lapack_interfaces.f90:(.text+0x59f): undefined reference to `dpptrs_'
external/lib/libpelib.a(pe_lapack_interfaces.f90.o): In function `__pe_lapack_interfaces_MOD_pptri':
pe_lapack_interfaces.f90:(.text+0x685): undefined reference to `dpptri_'
external/lib/libpelib.a(pe_lapack_interfaces.f90.o): In function `__pe_lapack_interfaces_MOD_pptrf':
pe_lapack_interfaces.f90:(.text+0x765): undefined reference to `dpptrf_'
external/lib/libpelib.a(pe_lapack_interfaces.f90.o): In function `__pe_lapack_interfaces_MOD_sptrs':
pe_lapack_interfaces.f90:(.text+0x894): undefined reference to `dsptrs_'
external/lib/libpelib.a(pe_lapack_interfaces.f90.o): In function `__pe_lapack_interfaces_MOD_sptri':
pe_lapack_interfaces.f90:(.text+0x9bf): undefined reference to `dsptri_'
external/lib/libpelib.a(pe_lapack_interfaces.f90.o): In function `__pe_lapack_interfaces_MOD_sptrf':
pe_lapack_interfaces.f90:(.text+0xb1b): undefined reference to `dsptrf_'
pe_lapack_interfaces.f90:(.text+0xbad): undefined reference to `dsptrf_'
/lib64/atlas/liblapack.a(ATL_dgetrfC.o): In function `ATL_dgetrfC':
(.text+0x124): undefined reference to `cblas_dtrsm'
/lib64/atlas/liblapack.a(ATL_dgetrfC.o): In function `ATL_dgetrfC':
(.text+0x17b): undefined reference to `cblas_dgemm'
/lib64/atlas/liblapack.a(ATL_dgetrfC.o): In function `ATL_dgetrfC':
(.text+0x24d): undefined reference to `cblas_idamax'
/lib64/atlas/liblapack.a(ATL_dgetrfC.o): In function `ATL_dgetrfC':
(.text+0x2f8): undefined reference to `cblas_idamax'
/lib64/atlas/liblapack.a(ATL_dgetrfC.o): In function `ATL_dgetrfC':
(.text+0x406): undefined reference to `cblas_idamax'
/lib64/atlas/liblapack.a(ATL_dgetrfC.o): In function `ATL_dgetrfC':
(.text+0x51c): undefined reference to `cblas_dtrsm'
/lib64/atlas/liblapack.a(ATL_dgetrfC.o): In function `ATL_dgetrfC':
(.text+0x692): undefined reference to `cblas_dscal'
/lib64/atlas/liblapack.a(ATL_dgetrfC.o): In function `ATL_dgetrfC':
(.text+0x71c): undefined reference to `cblas_dscal'
/lib64/atlas/liblapack.a(ATL_dgetrfC.o): In function `ATL_dgetrfC':
(.text+0x75f): undefined reference to `cblas_dscal'
/lib64/atlas/liblapack.a(ATL_dgetrfR.o): In function `ATL_dgetrfR':
(.text+0xe3): undefined reference to `cblas_dtrsm'
/lib64/atlas/liblapack.a(ATL_dgetrfR.o): In function `ATL_dgetrfR':
(.text+0x12c): undefined reference to `cblas_dgemm'
/lib64/atlas/liblapack.a(ATL_dgetrfR.o): In function `ATL_dgetrfR':
(.text+0x1f4): undefined reference to `cblas_idamax'
/lib64/atlas/liblapack.a(ATL_dgetrfR.o): In function `ATL_dgetrfR':
(.text+0x288): undefined reference to `cblas_dscal'
/lib64/atlas/liblapack.a(ATL_dgetriC.o): In function `ATL_dgetriC':
(.text+0x157): undefined reference to `cblas_dtrsm'
/lib64/atlas/liblapack.a(ATL_dgetriC.o): In function `ATL_dgetriC':
(.text+0x295): undefined reference to `cblas_dgemm'
/lib64/atlas/liblapack.a(ATL_dgetriC.o): In function `ATL_dgetriC':
(.text+0x2d3): undefined reference to `cblas_dtrsm'
/lib64/atlas/liblapack.a(ATL_dgetriC.o): In function `ATL_dgetriC':
(.text+0x356): undefined reference to `cblas_dswap'
/lib64/atlas/liblapack.a(ATL_dgetriR.o): In function `ATL_dgetriR':
(.text+0x163): undefined reference to `cblas_dtrsm'
/lib64/atlas/liblapack.a(ATL_dgetriR.o): In function `ATL_dgetriR':
(.text+0x2a7): undefined reference to `cblas_dgemm'
/lib64/atlas/liblapack.a(ATL_dgetriR.o): In function `ATL_dgetriR':
(.text+0x2e6): undefined reference to `cblas_dtrsm'
/lib64/atlas/liblapack.a(ATL_dgetriR.o): In function `ATL_dgetriR':
(.text+0x36e): undefined reference to `cblas_dswap'
/lib64/atlas/liblapack.a(ATL_dgetrs.o): In function `ATL_dgetrs':
(.text+0x9c): undefined reference to `cblas_dtrsm'
/lib64/atlas/liblapack.a(ATL_dgetrs.o): In function `ATL_dgetrs':
(.text+0xd6): undefined reference to `cblas_dtrsm'
/lib64/atlas/liblapack.a(ATL_dgetrs.o): In function `ATL_dgetrs':
(.text+0x132): undefined reference to `cblas_dtrsm'
/lib64/atlas/liblapack.a(ATL_dgetrs.o): In function `ATL_dgetrs':
(.text+0x16a): undefined reference to `cblas_dtrsm'
/lib64/atlas/liblapack.a(ATL_dgetrs.o): In function `ATL_dgetrs':
(.text+0x1df): undefined reference to `cblas_dtrsm'
/lib64/atlas/liblapack.a(ATL_dgetrs.o):(.text+0x26c): more undefined references to `cblas_dtrsm' follow
/lib64/atlas/liblapack.a(ATL_ilaenv.o): In function `ATL_ilaenv':
(.text+0x44b): undefined reference to `ATL_zGetNB'
/lib64/atlas/liblapack.a(ATL_ilaenv.o): In function `ATL_ilaenv':
(.text+0x506): undefined reference to `ATL_sGetNB'
/lib64/atlas/liblapack.a(ATL_ilaenv.o): In function `ATL_ilaenv':
(.text+0x52b): undefined reference to `ATL_sGetNB'
/lib64/atlas/liblapack.a(ATL_ilaenv.o): In function `ATL_ilaenv':
(.text+0x571): undefined reference to `ATL_dGetNB'
/lib64/atlas/liblapack.a(ATL_ilaenv.o): In function `ATL_ilaenv':
(.text+0x59d): undefined reference to `ATL_dGetNB'
/lib64/atlas/liblapack.a(ATL_ilaenv.o): In function `ATL_ilaenv':
(.text+0x5b3): undefined reference to `ATL_cGetNB'
/lib64/atlas/liblapack.a(ATL_ilaenv.o): In function `ATL_ilaenv':
(.text+0x63c): undefined reference to `ATL_cGetNB'
/lib64/atlas/liblapack.a(ATL_ilaenv.o): In function `ATL_ilaenv':
(.text+0x6e7): undefined reference to `ATL_zGetNB'
/lib64/atlas/liblapack.a(ATL_dgetf2.o): In function `ATL_dgetf2':
(.text+0xa0): undefined reference to `cblas_idamax'
/lib64/atlas/liblapack.a(ATL_dgetf2.o): In function `ATL_dgetf2':
(.text+0xfc): undefined reference to `cblas_dswap'
/lib64/atlas/liblapack.a(ATL_dgetf2.o): In function `ATL_dgetf2':
(.text+0x17d): undefined reference to `ATL_dger'
/lib64/atlas/liblapack.a(ATL_dgetf2.o): In function `ATL_dgetf2':
(.text+0x217): undefined reference to `cblas_dscal'
collect2: error: ld returned 1 exit status
CMakeFiles/dalton.x.dir/build.make:102: recipe for target 'dalton.x' failed
make[2]: *** [dalton.x] Error 1
CMakeFiles/Makefile2:1341: recipe for target 'CMakeFiles/dalton.x.dir/all' failed
make[1]: *** [CMakeFiles/dalton.x.dir/all] Error 2
Makefile:138: recipe for target 'all' failed
make: *** [all] Error 2

Does anyone know how to deal with this?
Here is my ./setup command:

Code: Select all

$ ./setup --blas=auto --lapack=auto --omp --prefix=/home/henrique/bin/dalton

and here are the last lines of my setup command:

Code: Select all

-- Performing Test COMPILER_UNDERSTANDS_FORTRAN03
-- Performing Test COMPILER_UNDERSTANDS_FORTRAN03 - Success
-- Performing Test PTR_RESHAPE_WORKS
-- Performing Test PTR_RESHAPE_WORKS - Success
-- Math lib search order is MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE
-- You can select a specific type by defining for instance -D BLAS_TYPE=ATLAS or -D LAPACK_TYPE=ACML
-- or by redefining MATH_LIB_SEARCH_ORDER
-- Found BLAS: ATLAS (/lib64/atlas/libf77blas.a;/lib64/atlas/libcblas.a;/lib64/atlas/libatlas.a)
-- Found LAPACK: OPENBLAS (/lib64/atlas/libatlas.a;/lib64/atlas/liblapack.a)
-- Configuring done
-- Generating done
-- Build files have been written to: /home/henrique/Build/DALTON2016.2-Source/build

   configure step is done
   now you need to compile the sources:
   $ cd build
   $ make

Any help is much appreciated.

[Henrique]

Also a compilation problem with LSDalton:

Code: Select all

[ 77%] Building Fortran object CMakeFiles/declib.dir/src/deccc/rimp2.F90.o
/home/henrique/Build/lsdalton/src/deccc/rimp2.F90:170:14:

    type(c_ptr), target :: handle_cptr
              1
Error: Type name 'c_ptr' at (1) is ambiguous
/home/henrique/Build/lsdalton/src/deccc/rimp2.F90:171:14:

    type(c_ptr) :: cublas_handle
              1
Error: Type name 'c_ptr' at (1) is ambiguous
/home/henrique/Build/lsdalton/src/deccc/rimp2.F90:3211:14:

    type(c_ptr) :: cublas_handle
              1
Error: Type name 'c_ptr' at (1) is ambiguous
/home/henrique/Build/lsdalton/src/deccc/rimp2.F90:1055:108:

                      & int((i8*K)*M,kind=8),int(K*(N*i8),kind=8),int(M*(N*i8),kind=8),async_id,cublas_handle)
                                                                                                            1
Error: Symbol ‘cublas_handle’ at (1) has no IMPLICIT type
CMakeFiles/declib.dir/build.make:130: recipe for target 'CMakeFiles/declib.dir/src/deccc/rimp2.F90.o' failed
make[3]: *** [CMakeFiles/declib.dir/src/deccc/rimp2.F90.o] Error 1
CMakeFiles/declib.dir/build.make:146: recipe for target 'CMakeFiles/declib.dir/src/deccc/rimp2.F90.o.provides' failed
make[2]: *** [CMakeFiles/declib.dir/src/deccc/rimp2.F90.o.provides] Error 2
CMakeFiles/Makefile2:1049: recipe for target 'CMakeFiles/declib.dir/all' failed
make[1]: *** [CMakeFiles/declib.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2

[bast]

I have fixed the problem in LSDalton in the development version some time ago like this (the "+" mark added lines):

Code: Select all

Author: Radovan Bast <bast@users.noreply.github.com>
Date:   Thu Aug 4 15:43:07 2016 +0200

    restore compilation with gcc 6.1.1; fixes #53

diff --git a/src/deccc/rimp2.F90 b/src/deccc/rimp2.F90
index 65c4cbf..14f7bff 100644
--- a/src/deccc/rimp2.F90
+++ b/src/deccc/rimp2.F90
@@ -102,6 +102,7 @@ end subroutine decnp_RIMP2_integrals_and_amplitudes
 subroutine RIMP2_integrals_and_amplitudes(MyFragment,&
       & goccEOS, toccEOS,gvirtEOS, tvirtEOS, djik,blad)
 
+   use iso_c_binding, only: c_ptr
    implicit none
    !> Atomic fragment (or pair fragment)
    type(decfrag), intent(inout) :: MyFragment
@@ -2445,6 +2446,7 @@ end subroutine BuildEosArrayVirt
 !> \author Thomas Kjaergaard
 !> \date Marts 2016
 subroutine SOSRIMP2_energy(MyFragment)
+   use iso_c_binding, only: c_ptr
    implicit none
    !> Atomic fragment (or pair fragment)
    type(decfrag), intent(inout) :: MyFragment
@@ -4199,6 +4201,7 @@ end subroutine BuildTampLaplaceCPU
 !> \author Thomas Kjaergaard
 !> \date August 2015
 subroutine RIMP2F12_Ccoupling_energy(MyFragment,EnergyF12Ccoupling,Fragment1,Fragment2)
+   use iso_c_binding, only: c_ptr
    implicit none
    !> Atomic fragment (or pair fragment)
    type(decfrag), intent(inout) :: MyFragment
@@ -5066,6 +5069,7 @@ end subroutine RIMP2F12_EnergyCont
 !> \author Thomas Kjaergaard
 !> \date 2015
 subroutine PerformAuxReduction(MyFragment)
+   use iso_c_binding, only: c_ptr
    implicit none
    !> Atomic fragment (or pair fragment)
    type(decfrag), intent(inout) :: MyFragment
@@ -5656,6 +5660,7 @@ end subroutine PerformAuxReduction
 subroutine BuildLTRIMP2OccModifiedFitCoeff(NBA,noccOut,nvirt,nvirt8,nLaplace,Ctmp2,use_bg_buf,&
      & UseGPU,nocc,nocc8,Calpha,TauOcc,UoccT,UoccEOST,TauVirt,UvirtT,async_id,cublas_handle,&
      & CtmpTmpArray,CtmpIn)
+  use iso_c_binding, only: c_ptr
   implicit none
   integer,intent(in) :: NBA,noccOut,nvirt,nLaplace,nocc
   integer(kind=8),intent(in) :: nvirt8,nocc8
@@ -5775,6 +5780,7 @@ end subroutine BuildLTRIMP2OccModifiedFitCoeff
 !> \date 2016
 subroutine BuildRIMP2OccFitCoeff(NBA,noccOut,nvirt,CalphaOut,use_bg_buf,&
      & UseGPU,nocc,Calpha,UoccEOST,UvirtT,async_id,cublas_handle)
+  use iso_c_binding, only: c_ptr
   implicit none
   integer,intent(in) :: NBA,noccOut,nvirt,nocc
   real(realk),intent(in) :: Calpha(NBA*nvirt*i8*nocc) 
@@ -5851,6 +5857,7 @@ end subroutine BuildRIMP2OccFitCoeff
 subroutine BuildLTRIMP2VirtModifiedFitCoeff(NBA,nocc,nvirtOut,nvirt8,nLaplace,Ctmp2,use_bg_buf,&
      & UseGPU,nvirt,nocc8,Calpha,TauOcc,UoccT,TauVirt,UvirtT,UvirtEOST,async_id,cublas_handle,&
      & CtmpTmpArray,CtmpIn)
+  use iso_c_binding, only: c_ptr
   implicit none
   integer,intent(in) :: NBA,nocc,nvirtOut,nLaplace,nvirt
   integer(kind=8),intent(in) :: nvirt8,nocc8
@@ -5965,6 +5972,7 @@ end subroutine BuildLTRIMP2VirtModifiedFitCoeff
 subroutine BuildRIMP2VirtFitCoeff(NBA,nvirt,nvirtOut,Calpha3,use_bg_buf,&
      & UseGPU,nocc,Calpha,UoccT,UvirtEOST,async_id,cublas_handle)
 
+  use iso_c_binding, only: c_ptr
   implicit none
   integer,intent(in) :: NBA,nocc,nvirtOut,nvirt
   real(realk),intent(in) :: Calpha(NBA*nvirt*i8*nocc) 
@@ -6431,6 +6439,7 @@ end subroutine CalcEnergyCOSmpiPairVirt
 subroutine CalcEnergyCos(nLaplace,nvirt,noccOut,Ctmp2,Calpha3,mynum,numnodes,&
      & CollaborateWithSlaves,NBA,use_bg_buf,UseGPU,async_id,cublas_handle,&
      & PairW,EnergyCos,nbasisAux,laplaceW)
+  use iso_c_binding, only: c_ptr
   implicit none
   !> number of auxiliary basis functions
   integer,intent(in) :: nbasisAux
@@ -6569,6 +6578,7 @@ end subroutine CalcEnergyCos
 subroutine ConstructWalphabetaAuxRed(Walphabeta,nbasisAux,nLaplace,nvirt,noccOut,&
      & Ctmp2,Calpha3,mynum,numnodes,CollaborateWithSlaves,NBA,use_bg_buf,UseGPU,&
      & async_id,cublas_handle,PairW,TensorTiling3C)
+  use iso_c_binding, only: c_ptr
   implicit none
   !> number of auxiliary basis functions
   integer,intent(in) :: nbasisAux
@@ -6858,6 +6868,7 @@ end subroutine PlugWtmpIntoWfullMPI
 !> \date 2016
 subroutine ConstructWalphabetaAuxRedOwn(Wtmp,NBA,nLaplace,nvirt,nocc,&
      & Ctmp2,Calpha3,UseGPU,async_id,cublas_handle,PairW)
+  use iso_c_binding, only: c_ptr
   implicit none
   !> number of auxiliary basis functions assigned to this node
   integer,intent(in) :: NBA
@@ -6927,6 +6938,7 @@ end subroutine ConstructWalphabetaAuxRedOwn
 !> \date 2016
 subroutine ConstructWalphabetaAuxRedOwnPair(Wtmp,NBA,nLaplace,nvirt,nocc,&
      & Ctmp2,Calpha3,UseGPU,async_id,cublas_handle,DoEosP)
+  use iso_c_binding, only: c_ptr
   implicit none
   !> number of auxiliary basis functions assigned to this node
   integer,intent(in) :: NBA
@@ -6996,6 +7008,7 @@ end subroutine ConstructWalphabetaAuxRedOwnPair
 !> \date 2016
 subroutine ConstructWalphabetaAuxRedMPI(Wtmp,NBA,nLaplace,nvirt,nocc,&
      & Ctmp2,Cmpi,NBAmpi,UseGPU,async_id,cublas_handle,PairW)
+  use iso_c_binding, only: c_ptr
   implicit none
   !> number of auxiliary basis functions assigned to this node
   integer,intent(in) :: NBA
@@ -7064,6 +7077,7 @@ end subroutine ConstructWalphabetaAuxRedMPI
 !> \date 2016
 subroutine ConstructWalphabetaAuxRedMPIpair(Wtmp,NBA,nLaplace,nvirt,nocc,&
      & Ctmp2,Cmpi,NBAmpi,UseGPU,async_id,cublas_handle,DoEosP)
+  use iso_c_binding, only: c_ptr
   implicit none
   !> number of auxiliary basis functions assigned to this node
   integer,intent(in) :: NBA

[bast]

[quote="Henrique"]

Code: Select all

-- Performing Test COMPILER_UNDERSTANDS_FORTRAN03
-- Performing Test COMPILER_UNDERSTANDS_FORTRAN03 - Success
-- Performing Test PTR_RESHAPE_WORKS
-- Performing Test PTR_RESHAPE_WORKS - Success
-- Math lib search order is MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE
-- You can select a specific type by defining for instance -D BLAS_TYPE=ATLAS or -D LAPACK_TYPE=ACML
-- or by redefining MATH_LIB_SEARCH_ORDER
-- Found BLAS: ATLAS (/lib64/atlas/libf77blas.a;/lib64/atlas/libcblas.a;/lib64/atlas/libatlas.a)
-- Found LAPACK: OPENBLAS (/lib64/atlas/libatlas.a;/lib64/atlas/liblapack.a)
-- Configuring done
-- Generating done
-- Build files have been written to: /home/henrique/Build/DALTON2016.2-Source/build

   configure step is done
   now you need to compile the sources:
   $ cd build
   $ make

It looks like linking to LAPACK fails. Also the detection looks strange since the configuration reports that it found OpenBLAS but then
links to ATLAS. I would try explicit linking or internal math libraries to get started. I would check with nm whether the lapack library contains
the symbols that Dalton tries to link to.