From tradke at aei.mpg.de Fri Feb 2 09:35:47 2007 From: tradke at aei.mpg.de (Thomas Radke) Date: Fri, 02 Feb 2007 16:35:47 +0100 Subject: [Users] Launch of Cactus User Portal Message-ID: <45C35A53.6000607@aei.mpg.de> Hi, I'm pleased to announce the launch of the Cactus User Portal, a service for users and developers of the Cactus code to publish and share Cactus-related information of common interest. Version 1.0 of the portal provides functionality to access and query results from integration tests on selected production machines at AEI and CCT. The integration tests include the Cactus flesh and all Cactus arrangements as well as other publicly available modules such as AEIThorns, Carpet, and TAT. Each nightly test 1) checks out flesh and thorns from in their latest version from CVS/darcs 2) creates a configuration called 'PublicThorns' 3) builds it according to the given thornlist 4) also builds all utility programs associated with thorns 5) runs all available testsuites Integration test results from currently 4 machines are presented in the portal and can be queried in various ways. Portal access is provided through a predefined guest user account. The Cactus User Portal is available on https://portal.cactuscode.org. -- Cheers, Thomas. From heeilkim at gmail.com Mon Feb 12 01:13:12 2007 From: heeilkim at gmail.com (Hee Il Kim) Date: Mon, 12 Feb 2007 16:13:12 +0900 Subject: [Users] several questions on pugh Message-ID: Hi, I have several questions about pugh. When I run a 64 cubed single cpu simulation, the cactus run shows INFO (CartGrid3D): x=>[0,63] y=>[0,63] z=>[0,63] INFO (PUGH): MPI Evolution on 1 processors INFO (PUGH): 3-dimensional grid functions INFO (PUGH): Size: 64 64 64 INFO (PUGH): Processor topology: 1 x 1 x 1 INFO (PUGH): Local load: 262144 [64 x 64 x 64] Nothing strange. But when I make a mpirun, for example, using 8 cpus (=8 cpu cores), INFO (CartGrid3D): x=>[0,63] y=>[0,63] z=>[0,63] INFO (PUGH): MPI Evolution on 8 processors INFO (PUGH): 3-dimensional grid functions INFO (PUGH): Size: 64 64 64 INFO (PUGH): Processor topology: 2 x 2 x 2 INFO (PUGH): Local load: 35937 [33 x 33 x 33] Why is the local load 33x33x33? I think it should be 32x32x32 or 34x34x34 if it includes ghostzones with stencil 1 ? I can get a correct result even with this problem. What does the local load represent? In order to look into further, I tried to use CCTK_MyProcs function. But I only get rank 0. In fact I don't know how to display the rank of computing node cpus. I tried "-r[o|e]" option for cactus run but no lucks. I'm using 6 node intel dual core (presler 930) cluster. I use Cactus for numerical relativity but I'm a newbie on computational science. I appreciate your kind helps in advance. Kim, Hee Il from Korea heeilkim at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.cactuscode.org/pipermail/users/attachments/20070212/ed581198/attachment.html From goodale at cct.lsu.edu Mon Feb 12 01:43:24 2007 From: goodale at cct.lsu.edu (Tom Goodale) Date: Mon, 12 Feb 2007 07:43:24 +0000 (GMT) Subject: [Users] several questions on pugh In-Reply-To: References: Message-ID: Hi, you only need ghost-zones on internal processor boundaries. So with 9 procs you get 2x2x2 procs with 32 physical points each and one ghost zone each. Cheers, Tom On Mon, 12 Feb 2007, Hee Il Kim wrote: > Hi, > > I have several questions about pugh. When I run a 64 cubed single > cpu simulation, the cactus run shows > > INFO (CartGrid3D): x=>[0,63] y=>[0,63] z=>[0,63] > INFO (PUGH): MPI Evolution on 1 processors > INFO (PUGH): 3-dimensional grid functions > INFO (PUGH): Size: 64 64 64 > INFO (PUGH): Processor topology: 1 x 1 x 1 > INFO (PUGH): Local load: 262144 [64 x 64 x 64] > > Nothing strange. But when I make a mpirun, for example, using 8 cpus (=8 cpu > cores), > > INFO (CartGrid3D): x=>[0,63] y=>[0,63] z=>[0,63] > INFO (PUGH): MPI Evolution on 8 processors > INFO (PUGH): 3-dimensional grid functions > INFO (PUGH): Size: 64 64 64 > INFO (PUGH): Processor topology: 2 x 2 x 2 > INFO (PUGH): Local load: 35937 [33 x 33 x 33] > > Why is the local load 33x33x33? I think it should be 32x32x32 or 34x34x34 > if it includes ghostzones with stencil 1 ? I can get a correct result even > with this problem. What does the local load represent? > > In order to look into further, I tried to use CCTK_MyProcs function. But I > only get rank 0. In fact I don't know how to display the rank of computing > node cpus. I tried "-r[o|e]" option for cactus run but no lucks. > > I'm using 6 node intel dual core (presler 930) cluster. I use Cactus for > numerical relativity but I'm a newbie on computational science. I appreciate > your kind helps in advance. > > Kim, Hee Il > from Korea > heeilkim at gmail.com > From heeilkim at gmail.com Mon Feb 12 02:00:41 2007 From: heeilkim at gmail.com (Hee Il Kim) Date: Mon, 12 Feb 2007 17:00:41 +0900 Subject: [Users] several questions on pugh In-Reply-To: References: Message-ID: Thanks Tom, And I found CCTK_Proc#.out files were created. I emailed you before I had a very strange problem that I couldn't use all the cpu cores for some parameter files. I found that the problem seems to be caused by httpd thorn but cure in Cactus development version. I don't know the reason. Anyway thanks for your quick reply. Regards, Hee Il 2007/2/12, Tom Goodale : > > Hi, > > you only need ghost-zones on internal processor boundaries. So with 9 > procs you get 2x2x2 procs with 32 physical points each and one ghost zone > each. > > Cheers, > > Tom > > > On Mon, 12 Feb 2007, Hee Il Kim wrote: > > > Hi, > > > > I have several questions about pugh. When I run a 64 cubed single > > cpu simulation, the cactus run shows > > > > INFO (CartGrid3D): x=>[0,63] y=>[0,63] z=>[0,63] > > INFO (PUGH): MPI Evolution on 1 processors > > INFO (PUGH): 3-dimensional grid functions > > INFO (PUGH): Size: 64 64 64 > > INFO (PUGH): Processor topology: 1 x 1 x 1 > > INFO (PUGH): Local load: 262144 [64 x 64 x 64] > > > > Nothing strange. But when I make a mpirun, for example, using 8 cpus (=8 > cpu > > cores), > > > > INFO (CartGrid3D): x=>[0,63] y=>[0,63] z=>[0,63] > > INFO (PUGH): MPI Evolution on 8 processors > > INFO (PUGH): 3-dimensional grid functions > > INFO (PUGH): Size: 64 64 64 > > INFO (PUGH): Processor topology: 2 x 2 x 2 > > INFO (PUGH): Local load: 35937 [33 x 33 x 33] > > > > Why is the local load 33x33x33? I think it should be 32x32x32 or > 34x34x34 > > if it includes ghostzones with stencil 1 ? I can get a correct result > even > > with this problem. What does the local load represent? > > > > In order to look into further, I tried to use CCTK_MyProcs function. But > I > > only get rank 0. In fact I don't know how to display the rank of > computing > > node cpus. I tried "-r[o|e]" option for cactus run but no lucks. > > > > I'm using 6 node intel dual core (presler 930) cluster. I use Cactus for > > numerical relativity but I'm a newbie on computational science. I > appreciate > > your kind helps in advance. > > > > Kim, Hee Il > > from Korea > > heeilkim at gmail.com > > > _______________________________________________ > Users mailing list > Users at cactuscode.org > http://www.cactuscode.org/mailman/listinfo/users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.cactuscode.org/pipermail/users/attachments/20070212/9b3483c1/attachment.html From heeilkim at gmail.com Wed Feb 14 04:14:50 2007 From: heeilkim at gmail.com (Hee Il Kim) Date: Wed, 14 Feb 2007 19:14:50 +0900 Subject: [Users] extension name of ioascii output files Message-ID: Hi, In some cases, the extension names, tl, xl, yl, zl are used for output file names. What's the reason "asc" or "xg" are not used for the extension names as described in the thorn guide? Is there anyway to control the extension names? I couldn't find any crucial difference between the two cases in the parameter files. Regards, Hee Il -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.cactuscode.org/pipermail/users/attachments/20070214/ad267958/attachment.html From tradke at aei.mpg.de Wed Feb 14 10:27:09 2007 From: tradke at aei.mpg.de (Thomas Radke) Date: Wed, 14 Feb 2007 17:27:09 +0100 Subject: [Users] extension name of ioascii output files In-Reply-To: References: Message-ID: <45D3385D.5030006@aei.mpg.de> Hee Il Kim wrote: > Hi, > > In some cases, the extension names, tl, xl, yl, zl are used for output file > names. What's the reason "asc" or "xg" are not used for the extension names > as described in the thorn guide? Is there anyway to control the extension > names? I couldn't find any crucial difference between the two cases in the > parameter files. The reason for the "[txyzl]l" output file extensions is purely historical: they were used in Cactus 3. For backwards compatibility we kept them in Cactus 4, however you can switch to using the new filename extensions by setting IO::new_filename_scheme = "yes" in your parameter files. -- Cheers, Thomas. From hawleys at mail.belmont.edu Sun Feb 18 12:09:40 2007 From: hawleys at mail.belmont.edu (Scott Hawley) Date: Sun, 18 Feb 2007 12:09:40 -0600 Subject: [Users] Help w/ MPI link errors Message-ID: <5470FC44-E319-4760-96EF-0E18C52FB1C2@mail.belmont.edu> Hi. I'm having a bunch of errors when I try to link Cactus on my new machine. It's running Red Hat Enterprise Linux 4. I think there's something wrong with my installation of MPI, (LAM 7.1.2/MPI 2 ), but I'm not sure what it is. If anyone is willing to help, see the link errors below. To help me get linked running, in return I'd be willing to let someone (someone I know) have an account on the machine (quad core 3.4GHz, 8 Gigs of RAM, and is currently extremely underused because I'm teaching so much of the time) to use for their own projects. Thanks, Scott -- Scott H. Hawley, Ph.D. Asst. Prof. of Physics Chemistry & Physics Dept Office: Hitch 100D Belmont University Tel: +1-615-460-6206 Nashville, TN 37212 USA Fax: +1-615-460-5458 > gmake texmex SILENT=no ... ... Creating cactus_texmex in /home/shawley/Cactus/exe from CactusEinstein/ADMAnalysis CactusEinstein/ADMBase CactusEinstein/ ADMConstraints CactusEinstein/ADMCoupling CactusEinstein/ADMMacros AEIThorns/AEILocalInterp AEIThorns/AHFinderDirect AEIThorns/BSSN_MoL CactusBase/Boundary Carpet/Carpet Carpet/CarpetIOASCII Carpet/ CarpetIOHDF5 Carpet/CarpetIOScalar Carpet/CarpetInterp Carpet/ CarpetLib Carpet/CarpetReduce Carpet/CarpetRegrid Carpet/CarpetSlab CactusBase/CartGrid3D CactusBase/CoordBase CactusEinstein/CoordGauge AEIThorns/Dissipation AEIThorns/Exact CactusEinstein/Extract AEIThorns/Fortran AEIThorns/IDFileADM AEIDevelopment/IDPuncture CactusBase/IOASCII CactusBase/IOBasic CactusBase/IOUtil Excision/ LegoExcision CactusBase/LocalInterp CactusBase/LocalReduce CactusBase/ MoL CactusUtils/NaNChecker AEIThorns/Nice AEIThorns/Noise CactusEinstein/PsiKadelia TAT/Slab CactusEinstein/SpaceMask AEIThorns/ SphericalSurface CactusEinstein/StaticConformal CactusBase/SymBase TAT/TATelliptic AEIThorns/TensorTypes AEIDevelopment/TexMEx CactusBase/Time CactusEinstein/TimeGeodesic CactusUtils/TimerReport datetime=`/bin/date +'%Y-%m-%dT%H:%M:%S%z' 2>&1` ; \ if [ $? != 0 ]; then datetime=`/bin/date` ; fi ; \ gcc4 -I/sw/include -I/Users/shawley/include -O2 - DCCTK_COMPILE_DATETIME="$datetime" -c -o "/home/shawley/Cactus/ configs/texmex/datestamp.o" -I"/home/shawley/Cactus/src/include" -I"/ home/shawley/Cactus/configs/texmex/config-data" "/home/shawley/Cactus/ src/datestamp.c" if [ ! -d /home/shawley/Cactus/exe ]; then mkdir -p /home/shawley/ Cactus/exe ; fi g++4 -o "/home/shawley/Cactus/exe/cactus_texmex" -O2 -L/sw/lib -L/ Users/shawley/lib "/home/shawley/Cactus/configs/texmex/datestamp.o" - L/home/shawley/Cactus/configs/texmex/lib -lthorn_Cactus - lthorn_CactusBindings -lthorn_BSSN_MoL -lthorn_MoL -lthorn_NaNChecker -lthorn_CarpetReduce -lthorn_Exact -lthorn_TexMEx - lthorn_CarpetIOScalar -lthorn_IOBasic -lthorn_TimerReport - lthorn_Time -lthorn_TensorTypes -lthorn_SymBase -lthorn_Slab - lthorn_Nice -lthorn_LocalReduce -lthorn_LocalInterp -lthorn_Fortran - lthorn_AEILocalInterp -lthorn_ADMCoupling -lthorn_CarpetInterp - lthorn_CarpetIOHDF5 -lthorn_Extract -lthorn_CarpetRegrid - lthorn_LegoExcision -lthorn_TimeGeodesic -lthorn_CoordGauge - lthorn_CarpetIOASCII -lthorn_ADMAnalysis -lthorn_CarpetSlab - lthorn_Carpet -lthorn_CarpetLib -lthorn_Dissipation - lthorn_IDPuncture -lthorn_TATelliptic -lthorn_IOASCII - lthorn_AHFinderDirect -lthorn_SphericalSurface -lthorn_IDFileADM - lthorn_IOUtil -lthorn_ADMConstraints -lthorn_SpaceMask -lthorn_Noise - lthorn_PsiKadelia -lthorn_StaticConformal -lthorn_ADMBase - lthorn_CartGrid3D -lthorn_CoordBase -lthorn_Boundary - lthorn_ADMMacros -lthorn_Cactus -lthorn_CactusBindings -L/usr/local/ hdf5/lib -L/usr/local/lib -L/home/shawley/texmex//lib -L/usr/lib/gcc/ x86_64-redhat-linux/4.1.0 -lhdf5 -lz -lm -lmpi -llam -llammpi++ - lpthread -lutil -ldl -ltexmex -lcrypt -lgfortran /usr/local/lib/liblammpi++.a(intercepts.o)(.text+0x6f): In function `throw_excptn_fctn': : undefined reference to `MPI_Error_class' /usr/local/lib/liblammpi++.a(datatype.o)(.text+0x45d): In function `MPI::Datatype::Create_keyval(int (*)(MPI::Datatype const&, int, void*, void const*, void*, bool&), int (*)(MPI::Datatype&, int, void*, void*), void*)': : undefined reference to `MPI_Type_create_keyval' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x3a): In function `MPI::Detach_buffer(void*&)': : undefined reference to `MPI_Buffer_detach' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x8a): In function `MPI::Get_error_class(int)': : undefined reference to `MPI_Error_class' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x140): In function `MPI::Init_thread(int)': : undefined reference to `MPI_Init_thread' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x151): In function `MPI::Init_thread(int)': : undefined reference to `MPI_Errhandler_create' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x16a): In function `MPI::Init_thread(int&, char**&, int)': : undefined reference to `MPI_Init_thread' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x17b): In function `MPI::Init_thread(int&, char**&, int)': : undefined reference to `MPI_Errhandler_create' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x19a): In function `MPI::Is_thread_main()': : undefined reference to `MPI_Is_thread_main' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x1ba): In function `MPI::Query_thread()': : undefined reference to `MPI_Query_thread' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x1dc): In function `MPI::Alloc_mem(long, MPI::Info const&)': : undefined reference to `MPI_Alloc_mem' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x308): In function `MPI::Get_address(void*)': : undefined reference to `MPI_Get_address' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x21): In function `MPI::Attach_buffer(void*, int)': : undefined reference to `MPI_Buffer_attach' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x51): In function `MPI::Compute_dims(int, int, int*)': : undefined reference to `MPI_Dims_create' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x61): In function `MPI::Get_processor_name(char*, int&)': : undefined reference to `MPI_Get_processor_name' /usr/local/lib/liblammpi++.a(functions.o)(.text+0xb1): In function `MPI::Wtick()': : undefined reference to `MPI_Wtick' /usr/local/lib/liblammpi++.a(functions.o)(.text+0xda): In function `MPI::Init(int&, char**&)': : undefined reference to `MPI_Errhandler_create' /usr/local/lib/liblammpi++.a(functions.o)(.text+0xfe): In function `MPI::Init()': : undefined reference to `MPI_Errhandler_create' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x1f1): In function `MPI::Free_mem(void*)': : undefined reference to `MPI_Free_mem' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x201): In function `MPI::Close_port(char const*)': : undefined reference to `MPI_Close_port' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x215): In function `MPI::Lookup_name(char const*, MPI::Info const&, char*)': : undefined reference to `MPI_Lookup_name' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x225): In function `MPI::Open_port(MPI::Info const&, char*)': : undefined reference to `MPI_Open_port' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x235): In function `MPI::Publish_name(char const*, MPI::Info const&, char const*)': : undefined reference to `MPI_Publish_name' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x245): In function `MPI::Unpublish_name(char const*, MPI::Info const&, char const*)': : undefined reference to `MPI_Unpublish_name' /usr/local/lib/liblammpi++.a(functions.o)(.text+0x2f1): In function `MPI::Get_version(int&, int&)': : undefined reference to `MPI_Get_version' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZN4PMPI4Info6DeleteEPKc+0x5): In function `PMPI::Info::Delete(char const*)': : undefined reference to `MPI_Info_delete' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZNK4PMPI4Info3DupEv+0x12): In function `PMPI::Info::Dup() const': : undefined reference to `MPI_Info_dup' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZN4PMPI4Info4FreeEv+0x5): In function `PMPI::Info::Free()': : undefined reference to `MPI_Info_free' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZNK4PMPI4Info9Get_nkeysEv+0xe): In function `PMPI::Info::Get_nkeys() const': : undefined reference to `MPI_Info_get_nkeys' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZNK4PMPI4Info10Get_nthkeyEiPc+0x5): In function `PMPI::Info::Get_nthkey(int, char*) const': : undefined reference to `MPI_Info_get_nthkey' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZNK4PMPI4Info12Get_valuelenEPKcRi+0xe): In function `PMPI::Info::Get_valuelen(char const*, int&) const': : undefined reference to `MPI_Info_get_valuelen' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZN4PMPI4Info3SetEPKcS2_+0x5): In function `PMPI::Info::Set(char const*, char const*)': : undefined reference to `MPI_Info_set' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZNK4PMPI3Win14Get_errhandlerEv+0x12): In function `PMPI::Win::Get_errhandler() const': : undefined reference to `MPI_Win_get_errhandler' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZN4PMPI3Win14Set_errhandlerERKNS_10ErrhandlerE +0x9): In function `PMPI::Win::Set_errhandler(PMPI::Errhandler const&)': : undefined reference to `MPI_Win_set_errhandler' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZNK4PMPI3Win10AccumulateEPKviRKNS_8DatatypeEiliS5_RKNS _2OpE+0x45): In function `PMPI::Win::Accumulate(void const*, int, PMPI::Datatype const&, int, long, int, PMPI::Datatype const&, PMPI::Op const&) const': : undefined reference to `MPI_Accumulate' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZNK4PMPI3Win8CompleteEv+0x5): In function `PMPI::Win::Complete() const': : undefined reference to `MPI_Win_complete' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZNK4PMPI3Win5FenceEi+0x9): In function `PMPI::Win::Fence(int) const': : undefined reference to `MPI_Win_fence' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZN4PMPI3Win4FreeEv+0x5): In function `PMPI::Win::Free()': : undefined reference to `MPI_Win_free' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZNK4PMPI3Win3GetEPKviRKNS_8DatatypeEiliS5_+0x34): In function `PMPI::Win::Get(void const*, int, PMPI::Datatype const&, int, long, int, PMPI::Datatype const&) const': : undefined reference to `MPI_Get' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZNK4PMPI3Win9Get_groupEv+0x12): In function `PMPI::Win::Get_group() const': : undefined reference to `MPI_Win_get_group' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZNK4PMPI3Win4PostERKNS_5GroupEi+0xe): In function `PMPI::Win::Post(PMPI::Group const&, int) const': : undefined reference to `MPI_Win_post' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZNK4PMPI3Win3PutEPKviRKNS_8DatatypeEiliS5_+0x34): In function `PMPI::Win::Put(void const*, int, PMPI::Datatype const&, int, long, int, PMPI::Datatype const&) const': : undefined reference to `MPI_Put' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZNK4PMPI3Win5StartERKNS_5GroupEi+0xe): In function `PMPI::Win::Start(PMPI::Group const&, int) const': : undefined reference to `MPI_Win_start' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZNK4PMPI3Win4WaitEv+0x5): In function `PMPI::Win::Wait() const': : undefined reference to `MPI_Win_wait' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZN4PMPI3Win11Delete_attrEi+0x5): In function `PMPI::Win::Delete_attr(int)': : undefined reference to `MPI_Win_delete_attr' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZNK4PMPI3Win8Get_nameEPcRi+0x5): In function `PMPI::Win::Get_name(char*, int&) const': : undefined reference to `MPI_Win_get_name' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZN4PMPI3Win8Set_attrEiPKv+0x5): In function `PMPI::Win::Set_attr(int, void const*)': : undefined reference to `MPI_Win_set_attr' /usr/local/lib/liblammpi++.a(mpicxx.o) (.gnu.linkonce.t._ZN4PMPI3Win8Set_nameEPKc+0x5): In function `PMPI::Win::Set_name(char const*)': : undefined reference to `MPI_Win_set_name' /usr/local/lib/liblammpi++.a(intracomm.o)(.text+0x3e9): In function `MPI::Intracomm::Dup() const': : undefined reference to `MPI_Comm_dup' /usr/local/lib/liblammpi++.a(intracomm.o)(.text+0x476): In function `MPI::Intracomm::Clone() const': : undefined reference to `MPI_Comm_dup' /usr/local/lib/liblammpi++.a(topology.o)(.text+0x18): In function `MPI::Cartcomm::Dup() const': : undefined reference to `MPI_Comm_dup' /usr/local/lib/liblammpi++.a(topology.o)(.text+0x120): In function `MPI::Cartcomm::Clone() const': : undefined reference to `MPI_Comm_dup' /usr/local/lib/liblammpi++.a(topology.o)(.text+0x518): In function `MPI::Graphcomm::Dup() const': : undefined reference to `MPI_Comm_dup' /usr/local/lib/liblammpi++.a(topology.o)(.text+0x620): more undefined references to `MPI_Comm_dup' follow /usr/local/lib/liblammpi++.a(intercomm.o)(.text+0x142): In function `MPI::Intercomm::Get_remote_group() const': : undefined reference to `MPI_Comm_remote_group' /usr/local/lib/liblammpi++.a(info.o)(.text+0xe): In function `MPI::Info::Create()': : undefined reference to `MPI_Info_create' /usr/local/lib/liblammpi++.a(info.o)(.text+0x62): In function `MPI::Info::Dup() const': : undefined reference to `MPI_Info_dup' /usr/local/lib/liblammpi++.a(info.o)(.text+0xde): In function `MPI::Info::Get_nkeys() const': : undefined reference to `MPI_Info_get_nkeys' /usr/local/lib/liblammpi++.a(info.o)(.text+0x10e): In function `MPI::Info::Get_valuelen(char const*, int&) const': : undefined reference to `MPI_Info_get_valuelen' /usr/local/lib/liblammpi++.a(info.o)(.text+0x45): In function `MPI::Info::Delete(char const*)': : undefined reference to `MPI_Info_delete' /usr/local/lib/liblammpi++.a(info.o)(.text+0x95): In function `MPI::Info::Free()': : undefined reference to `MPI_Info_free' /usr/local/lib/liblammpi++.a(info.o)(.text+0xf5): In function `MPI::Info::Get_nthkey(int, char*) const': : undefined reference to `MPI_Info_get_nthkey' /usr/local/lib/liblammpi++.a(info.o)(.text+0x135): In function `MPI::Info::Set(char const*, char const*)': : undefined reference to `MPI_Info_set' /usr/local/lib/liblammpi++.a(win.o)(.text+0x11): In function `MPI::Win::Create_errhandler(void (*)(MPI::Win&, int*, ...))': : undefined reference to `MPI_Win_create_errhandler' /usr/local/lib/liblammpi++.a(win.o)(.text+0x62): In function `MPI::Win::Get_errhandler() const': : undefined reference to `MPI_Win_get_errhandler' /usr/local/lib/liblammpi++.a(win.o)(.text+0x141): In function `MPI::Win::Create(void const*, long, int, MPI::Info const&, MPI::Intracomm const&)': : undefined reference to `MPI_Win_create' /usr/local/lib/liblammpi++.a(win.o)(.text+0x1e2): In function `MPI::Win::Get_group() const': : undefined reference to `MPI_Win_get_group' /usr/local/lib/liblammpi++.a(win.o)(.text+0x2fa): In function `MPI::Win::Get_attr(MPI::Win const&, int, void*) const': : undefined reference to `MPI_Win_get_attr' /usr/local/lib/liblammpi++.a(win.o)(.text+0xa9): In function `MPI::Win::Set_errhandler(MPI::Errhandler const&)': : undefined reference to `MPI_Win_set_errhandler' /usr/local/lib/liblammpi++.a(win.o)(.text+0xfd): In function `MPI::Win::Accumulate(void const*, int, MPI::Datatype const&, int, long, int, MPI::Datatype const&, MPI::Op const&) const': : undefined reference to `MPI_Accumulate' /usr/local/lib/liblammpi++.a(win.o)(.text+0x115): In function `MPI::Win::Complete() const': : undefined reference to `MPI_Win_complete' /usr/local/lib/liblammpi++.a(win.o)(.text+0x179): In function `MPI::Win::Fence(int) const': : undefined reference to `MPI_Win_fence' /usr/local/lib/liblammpi++.a(win.o)(.text+0x185): In function `MPI::Win::Free()': : undefined reference to `MPI_Win_free' /usr/local/lib/liblammpi++.a(win.o)(.text+0x1c8): In function `MPI::Win::Get(void const*, int, MPI::Datatype const&, int, long, int, MPI::Datatype const&) const': : undefined reference to `MPI_Get' /usr/local/lib/liblammpi++.a(win.o)(.text+0x21e): In function `MPI::Win::Post(MPI::Group const&, int) const': : undefined reference to `MPI_Win_post' /usr/local/lib/liblammpi++.a(win.o)(.text+0x268): In function `MPI::Win::Put(void const*, int, MPI::Datatype const&, int, long, int, MPI::Datatype const&) const': : undefined reference to `MPI_Put' /usr/local/lib/liblammpi++.a(win.o)(.text+0x27e): In function `MPI::Win::Start(MPI::Group const&, int) const': : undefined reference to `MPI_Win_start' /usr/local/lib/liblammpi++.a(win.o)(.text+0x295): In function `MPI::Win::Wait() const': : undefined reference to `MPI_Win_wait' /usr/local/lib/liblammpi++.a(win.o)(.text+0x2c5): In function `MPI::Win::Delete_attr(int)': : undefined reference to `MPI_Win_delete_attr' /usr/local/lib/liblammpi++.a(win.o)(.text+0x2d1): In function `MPI::Win::Free_keyval(int&)': : undefined reference to `MPI_Win_free_keyval' /usr/local/lib/liblammpi++.a(win.o)(.text+0x315): In function `MPI::Win::Get_name(char*, int&) const': : undefined reference to `MPI_Win_get_name' /usr/local/lib/liblammpi++.a(win.o)(.text+0x325): In function `MPI::Win::Set_attr(int, void const*)': : undefined reference to `MPI_Win_set_attr' /usr/local/lib/liblammpi++.a(win.o)(.text+0x335): In function `MPI::Win::Set_name(char const*)': : undefined reference to `MPI_Win_set_name' /usr/local/lib/liblammpi++.a(request.o)(.text+0x3fd): In function `MPI::Request::Testany(int, MPI::Request*, int&, MPI::Status&)': : undefined reference to `MPI_Testany' /usr/local/lib/liblammpi++.a(request.o)(.text+0x558): In function `MPI::Request::Testany(int, MPI::Request*, int&)': : undefined reference to `MPI_Testany' /usr/local/lib/liblammpi++.a(request.o)(.text+0xaca): In function `MPI::Request::Testall(int, MPI::Request*, MPI::Status*)': : undefined reference to `MPI_Testall' /usr/local/lib/liblammpi++.a(request.o)(.text+0xcd1): In function `MPI::Request::Testall(int, MPI::Request*)': : undefined reference to `MPI_Testall' /usr/local/lib/liblammpi++.a(request.o)(.text+0xeb5): In function `MPI::Request::Waitsome(int, MPI::Request*, int*, MPI::Status*)': : undefined reference to `MPI_Waitsome' /usr/local/lib/liblammpi++.a(request.o)(.text+0x10b8): In function `MPI::Request::Waitsome(int, MPI::Request*, int*)': : undefined reference to `MPI_Waitsome' /usr/local/lib/liblammpi++.a(request.o)(.text+0x1295): In function `MPI::Request::Testsome(int, MPI::Request*, int*, MPI::Status*)': : undefined reference to `MPI_Testsome' /usr/local/lib/liblammpi++.a(request.o)(.text+0x1498): In function `MPI::Request::Testsome(int, MPI::Request*, int*)': : undefined reference to `MPI_Testsome' /usr/local/lib/liblammpi++.a(group.o)(.text+0x62): In function `MPI::Group::Compare(MPI::Group const&, MPI::Group const&)': : undefined reference to `MPI_Group_compare' /usr/local/lib/liblammpi++.a(group.o)(.text+0xdc): In function `MPI::Group::Intersect(MPI::Group const&, MPI::Group const&)': : undefined reference to `MPI_Group_intersection' /usr/local/lib/liblammpi++.a(group.o)(.text+0x12c): In function `MPI::Group::Difference(MPI::Group const&, MPI::Group const&)': : undefined reference to `MPI_Group_difference' /usr/local/lib/liblammpi++.a(group.o)(.text+0x49): In function `MPI::Group::Translate_ranks(MPI::Group const&, int, int const*, MPI::Group const&, int*)': : undefined reference to `MPI_Group_translate_ranks' /usr/local/lib/liblammpi++.a(comm.o)(.text+0x712): In function `MPI::Comm::Compare(MPI::Comm const&, MPI::Comm const&)': : undefined reference to `MPI_Comm_compare' /usr/local/lib/liblammpi++.a(comm.o)(.text+0x76e): In function `MPI::Comm::Get_parent()': : undefined reference to `MPI_Comm_get_parent' /usr/local/lib/liblammpi++.a(comm.o)(.text+0x7f0): In function `MPI::Comm::Join(int)': : undefined reference to `MPI_Comm_join' /usr/local/lib/liblammpi++.a(comm.o)(.text+0x8ff): In function `MPI::Comm::Create_errhandler(void (*)(MPI::Comm&, int*, ...))': : undefined reference to `MPI_Errhandler_create' /usr/local/lib/liblammpi++.a(comm.o)(.text+0x9ba): In function `MPI::Comm::DUP_FN(MPI::Comm const&, int, void*, void*, void*, bool&)': : undefined reference to `MPI_DUP_FN' /usr/local/lib/liblammpi++.a(comm.o)(.text+0xe9c): In function `MPI::Comm::Free_keyval(int&)': : undefined reference to `MPI_Keyval_free' /usr/local/lib/liblammpi++.a(comm.o)(.text+0x1063): In function `MPI::Comm::Create_keyval(int (*)(MPI::Comm const&, int, void*, void*, void*, bool&), int (*)(MPI::Comm&, int, void*, void*), void*)': : undefined reference to `MPI_Keyval_create' From I.Hawke at soton.ac.uk Sun Feb 18 12:37:30 2007 From: I.Hawke at soton.ac.uk (Ian Hawke) Date: Sun, 18 Feb 2007 18:37:30 +0000 Subject: [Users] Help w/ MPI link errors In-Reply-To: <5470FC44-E319-4760-96EF-0E18C52FB1C2@mail.belmont.edu> References: <5470FC44-E319-4760-96EF-0E18C52FB1C2@mail.belmont.edu> Message-ID: <45D89CEA.6000009@soton.ac.uk> Scott Hawley wrote: > Hi. I'm having a bunch of errors when I try to link Cactus on my new > machine. It's running Red Hat Enterprise Linux 4. I think there's > something wrong with my installation of MPI, (LAM 7.1.2/MPI 2 ), but > I'm not sure what it is. MPICH2 is not supported by default the last time I checked; Steve White did send a patch at one point (see http://www.cactuscode.org/pipermail/users/2006-April/001799.html ) but I don't think it was ever committed. I did try the patch at one point and it did work (modulo a minor change as I'd built MPICH2 with pthreads, so I had to add extra libraries). Steve, do you remember this? Ian From tradke at aei.mpg.de Mon Feb 19 03:49:04 2007 From: tradke at aei.mpg.de (Thomas Radke) Date: Mon, 19 Feb 2007 10:49:04 +0100 Subject: [Users] Help w/ MPI link errors In-Reply-To: <45D89CEA.6000009@soton.ac.uk> References: <5470FC44-E319-4760-96EF-0E18C52FB1C2@mail.belmont.edu> <45D89CEA.6000009@soton.ac.uk> Message-ID: <45D97290.8080302@aei.mpg.de> Ian Hawke wrote: > Scott Hawley wrote: > >>Hi. I'm having a bunch of errors when I try to link Cactus on my new >>machine. It's running Red Hat Enterprise Linux 4. I think there's >>something wrong with my installation of MPI, (LAM 7.1.2/MPI 2 ), but >>I'm not sure what it is. > > > MPICH2 is not supported by default the last time I checked; Steve White > did send a patch at one point (see > http://www.cactuscode.org/pipermail/users/2006-April/001799.html > ) but I don't think it was ever committed. I did try the patch at one > point and it did work (modulo a minor change as I'd built MPICH2 with > pthreads, so I had to add extra libraries). > > Steve, do you remember this? Steve's patch was about MPICH. From what I see in Scott's SILENT=no output, his problem is a wrong order of LAM libs: lammpi++ should appear _before_ anything else. I just fixed it, please update from CVS and try again. -- Cheers, Thomas. From sbrandt at cct.lsu.edu Wed Feb 21 02:50:05 2007 From: sbrandt at cct.lsu.edu (Steven R Brandt) Date: Wed, 21 Feb 2007 02:50:05 -0600 Subject: [Users] Help w/ MPI link errors In-Reply-To: <45D97290.8080302@aei.mpg.de> References: <5470FC44-E319-4760-96EF-0E18C52FB1C2@mail.belmont.edu> <45D89CEA.6000009@soton.ac.uk> <45D97290.8080302@aei.mpg.de> Message-ID: <45DC07BD.2030604@cct.lsu.edu> I think it turned out to be my error. I used gcc 4.0, but f77 (based on something older than 4.0). I told it not to use an f90 compiler. The mixed versions caused Cactus to get the link line mixed up (I could fix it by hand). The nature of the error messages, however, had me confused for a bit. Cheers, Steve Thomas Radke wrote: > Ian Hawke wrote: > >> Scott Hawley wrote: >> >> >>> Hi. I'm having a bunch of errors when I try to link Cactus on my new >>> machine. It's running Red Hat Enterprise Linux 4. I think there's >>> something wrong with my installation of MPI, (LAM 7.1.2/MPI 2 ), but >>> I'm not sure what it is. >>> >> MPICH2 is not supported by default the last time I checked; Steve White >> did send a patch at one point (see >> http://www.cactuscode.org/pipermail/users/2006-April/001799.html >> ) but I don't think it was ever committed. I did try the patch at one >> point and it did work (modulo a minor change as I'd built MPICH2 with >> pthreads, so I had to add extra libraries). >> >> Steve, do you remember this? >> > > Steve's patch was about MPICH. > > From what I see in Scott's SILENT=no output, his problem is a wrong > order of LAM libs: lammpi++ should appear _before_ anything else. > > I just fixed it, please update from CVS and try again. > >