Issues compiling the code on Geforce RTX 3090 with Cuda 11.4

[andreaswallberg]

Dear @rmingming ,

Thanks for making this interesting implementation of codeml available to the community. I have tried compiling it on a machine running Ubuntu 20.04 with Cuda 11.4 and a Geforce RTX 3090 (-arch=sm_86) but I can not get it to compile.

I first tried using hybrid settings in the Makefile:

### CONFIGURATION BGEIN ###
# =======================
CUDA_INSTALL_PATH =/usr/local/cuda-11.4
# set to your cuda installation path

SINGLE_GPU_ID    = 0    # the GPU card id which you want to use (id is from 0 to #GPUs-1)
# =======================
### CONFIGURATION END ###

# modify the following options if you want to use multiple GPU cards or GPU together with CPU
# ==================
MULTICARD_ONLY_GPU      = no    # yes if you want to use multiple GPU cards and not cooperate with CPU,if this entry is yes,HYBRID should be *no*
HYBRID                  = yes   # yes if you want to use GPU together with CPU (only available if MULTICARD_ONLY_GPU is *no*)
MAXGPU                  = 1     # the maximum number of GPU you want to use
MAXCPU                  = 40    # how many CPU cores to use (zero if you want to use *GPU only*), only available if HYBRID is *yes*
SSE                     = yes   # yes if your CPU support SSE, only available if HYBRID is *yes*

CC = cc # cc, gcc, cl
LIBS = -lm # -lM
NVCC = $(CUDA_INSTALL_PATH)/bin/nvcc
NVLIBS = -L$(CUDA_INSTALL_PATH)/lib64 -L$(CUDA_INSTALL_PATH)/lib -lcudart
NVFLAGS = -arch=sm_86

# ==================

I then get this error:

/usr/local/cuda-11.4/bin/nvcc -arch=sm_86 -DCUDA -DSTREAM -DHYBRID -DHYBRID_OR_MULTICARD -DMAXGPU=1      -DMAXCPU=40     -Xcompiler -pthread -Xcompiler -fopenmp -O3 -c cuda-codeml.cu
cuda-codeml.cu:76:61: error: alignment of array elements is greater than element size
   76 | double *__attribute((aligned(0x10))) nodes_conP[NNODE];
      |                                                             ^
cuda-codeml.cu: In function ‘void CUDA_ScheduleConditionalPNode(int, int, double*)’:
cuda-codeml.cu:1373:66: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 1373 |         if (pthread_create(&threads[dev_id], NULL, schedule, (void *) dev_id) != 0) {
      |                                                                  ^~~~~~
make: *** [Makefile:97: cuda-codeml.o] Error 1

If I turn of hybrid mode, I get further but eventually compilation fails again. Makefile:

### CONFIGURATION BGEIN ###
# =======================
CUDA_INSTALL_PATH =/usr/local/cuda-11.4
# set to your cuda installation path

SINGLE_GPU_ID    = 0    # the GPU card id which you want to use (id is from 0 to #GPUs-1)
# =======================
### CONFIGURATION END ###

# modify the following options if you want to use multiple GPU cards or GPU together with CPU
# ==================
MULTICARD_ONLY_GPU      = no    # yes if you want to use multiple GPU cards and not cooperate with CPU,if this entry is yes,HYBRID should be *no*
HYBRID                  = no    # yes if you want to use GPU together with CPU (only available if MULTICARD_ONLY_GPU is *no*)
MAXGPU                  = 1     # the maximum number of GPU you want to use
MAXCPU                  = 40    # how many CPU cores to use (zero if you want to use *GPU only*), only available if HYBRID is *yes*
SSE                     = yes   # yes if your CPU support SSE, only available if HYBRID is *yes*
# ==================

CC = cc # cc, gcc, cl
LIBS = -lm # -lM
NVCC = $(CUDA_INSTALL_PATH)/bin/nvcc
NVLIBS = -L$(CUDA_INSTALL_PATH)/lib64 -L$(CUDA_INSTALL_PATH)/lib -lcudart
NVFLAGS = -arch=sm_86

How it fails, after also printing a bunch of warnings:

cc  -DCUDA -DSTREAM -DSSE -O3 -funroll-loops -fomit-frame-pointer -lm  -L/usr/local/cuda-11.4/lib64 -L/usr/local/cuda-11.4/lib -lcudart -lstdc++ cuda-codeml.o tools.o codeml.o -o CuCodeML
/usr/bin/ld: codeml.o: in function `lfun2AA':
codeml.c:(.text+0x26a): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x287): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x2a4): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x2c1): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x2de): undefined reference to `exp'
/usr/bin/ld: codeml.o:codeml.c:(.text+0x2fc): more undefined references to `exp' follow
/usr/bin/ld: codeml.o: in function `lfun2AA':
codeml.c:(.text+0x611): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x691): undefined reference to `pow'
/usr/bin/ld: codeml.c:(.text+0x6c6): undefined reference to `pow'
/usr/bin/ld: codeml.c:(.text+0x703): undefined reference to `pow'
/usr/bin/ld: codeml.c:(.text+0x73f): undefined reference to `pow'
/usr/bin/ld: codeml.c:(.text+0x77b): undefined reference to `pow'
/usr/bin/ld: codeml.o:codeml.c:(.text+0x7b7): more undefined references to `pow' follow
/usr/bin/ld: codeml.o: in function `CDFdN_dS':
codeml.c:(.text+0xeb3): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0xec2): undefined reference to `exp'
/usr/bin/ld: codeml.o: in function `lfun2AArev':
codeml.c:(.text+0x1c01): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x1e8a): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x1eec): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x1f18): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x1f45): undefined reference to `log'
/usr/bin/ld: codeml.o:codeml.c:(.text+0x1f71): more undefined references to `log' follow
/usr/bin/ld: codeml.o: in function `DistanceMatNG86.constprop.0':
codeml.c:(.text+0x3734): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x37c9): undefined reference to `sqrt'
/usr/bin/ld: codeml.o: in function `PatternWeightSimple':
codeml.c:(.text+0x4c58): undefined reference to `pow'
/usr/bin/ld: codeml.o: in function `PatternWeight':
codeml.c:(.text+0x9a35): undefined reference to `pow'
/usr/bin/ld: codeml.o: in function `Chi2FreqHomo':
codeml.c:(.text+0xa46a): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0xa55f): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0xa5ad): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0xa5fe): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0xa64f): undefined reference to `log'
/usr/bin/ld: codeml.o:codeml.c:(.text+0xa69d): more undefined references to `log' follow
/usr/bin/ld: codeml.o: in function `DistanceMatNG86':
codeml.c:(.text+0x1105d): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x110fb): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x11144): undefined reference to `pow'
/usr/bin/ld: codeml.o: in function `OutputTimesRates':
codeml.c:(.text+0x1aeeb): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x1af02): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x1af19): undefined reference to `sqrt'
/usr/bin/ld: codeml.o: in function `rell':
codeml.c:(.text+0x262c3): undefined reference to `sqrt'
/usr/bin/ld: codeml.o: in function `ChangesSites':
codeml.c:(.text+0x26c3a): undefined reference to `pow'
/usr/bin/ld: codeml.c:(.text+0x26c67): undefined reference to `pow'
/usr/bin/ld: codeml.c:(.text+0x26f72): undefined reference to `pow'
/usr/bin/ld: codeml.c:(.text+0x26fa3): undefined reference to `pow'
/usr/bin/ld: codeml.o: in function `NodeScale':
codeml.c:(.text+0x27b50): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `funSS_AHRS':
codeml.c:(.text+0x2a495): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x2a4c3): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x2a4e6): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x2a605): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `GetLHistoryI':
codeml.c:(.text+0x31d5e): undefined reference to `sqrt'
/usr/bin/ld: codeml.o: in function `getpcodonClass':
codeml.c:(.text+0x37fdd): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x3802b): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x38079): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x380cd): undefined reference to `exp'
/usr/bin/ld: codeml.o: in function `GetCodonFreqs':
codeml.c:(.text+0x38ac2): undefined reference to `exp'
/usr/bin/ld: codeml.o:codeml.c:(.text+0x3919f): more undefined references to `exp' follow
/usr/bin/ld: codeml.o: in function `GetMutationMultiplier':
codeml.c:(.text+0x3afcd): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x3afdd): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `GetPMatBranch':
codeml.c:(.text+0x3bd94): undefined reference to `exp'
/usr/bin/ld: codeml.o: in function `GetInitialsCodon':
codeml.c:(.text+0x3df3f): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x3e125): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x3e2ca): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x3e33b): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x3e3b4): undefined reference to `log'
/usr/bin/ld: codeml.o:codeml.c:(.text+0x3e42b): more undefined references to `log' follow
/usr/bin/ld: codeml.o: in function `lfun2dSdN':
codeml.c:(.text+0x40d99): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x40dba): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x40ddb): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x40dfc): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x40e1d): undefined reference to `exp'
/usr/bin/ld: codeml.o:codeml.c:(.text+0x40e3e): more undefined references to `exp' follow
/usr/bin/ld: codeml.o: in function `lfun2dSdN':
codeml.c:(.text+0x41052): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x41413): undefined reference to `exp'
/usr/bin/ld: codeml.o: in function `logP':
codeml.c:(.text+0x414de): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x414ff): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x4158a): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x415ad): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `SelectionCoefficients':
codeml.c:(.text+0x42c18): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x43117): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x4315f): undefined reference to `exp'
/usr/bin/ld: codeml.o: in function `lfunt_SiteClass':
codeml.c:(.text+0x49362): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x495c9): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x4a2eb): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `lfuntdd_SiteClass':
codeml.c:(.text+0x4a971): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x4ad65): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x4bda2): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `lfunt':
codeml.c:(.text+0x4df65): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x4e8ba): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `lfuntdd':
codeml.c:(.text+0x4f0df): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x4fc2a): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `ProbSitePattern':
codeml.c:(.text+0x51c20): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x51c5d): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x51ce8): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x521c4): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `AdHocRateSmoothing':
codeml.c:(.text+0x559c7): undefined reference to `pow'
/usr/bin/ld: codeml.c:(.text+0x559d4): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x55a56): undefined reference to `pow'
/usr/bin/ld: codeml.c:(.text+0x5737c): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x57392): undefined reference to `sqrt'
/usr/bin/ld: codeml.o: in function `PostProbNode':
codeml.c:(.text+0x5780f): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x57d45): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x57e9a): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x589d5): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x590b8): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `PMatJC69like':
codeml.c:(.text+0x5937f): undefined reference to `exp'
/usr/bin/ld: codeml.o: in function `DetailOutput':
codeml.c:(.text+0x675c1): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x675f9): undefined reference to `sqrt'
/usr/bin/ld: codeml.o: in function `loglikelihood':
codeml.c:(.text+0x6772f): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `logistic_transformation':
codeml.c:(.text+0x677a0): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `logprior':
codeml.c:(.text+0x677ff): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x67819): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x67893): undefined reference to `log'
/usr/bin/ld: codeml.o:codeml.c:(.text+0x678b0): more undefined references to `log' follow
/usr/bin/ld: codeml.o: in function `BayesPairwise':
codeml.c:(.text+0x67fde): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x6818e): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x681a2): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x6827b): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x6828f): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x68333): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x68381): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x68589): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x6859d): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x68638): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x68686): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x68d52): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x68d6a): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x68e2e): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x68e9c): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x68fdf): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x69049): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x690e2): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x69102): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x691c6): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x691da): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x6946b): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x694ab): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x694f0): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x69528): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x6954b): undefined reference to `sqrt'
/usr/bin/ld: codeml.o: in function `CDFLogis':
codeml.c:(.text+0x69589): undefined reference to `exp'
/usr/bin/ld: codeml.o: in function `UpPassPPSG2000':
codeml.c:(.text+0x6b48a): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x6b67a): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x6b6ea): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x6bce0): undefined reference to `exp'
/usr/bin/ld: codeml.o: in function `AncestralJointPPSG2000':
codeml.c:(.text+0x6ca32): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `print_lnf_site':
codeml.c:(.text+0x6cbf4): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x6cc05): undefined reference to `exp'
/usr/bin/ld: codeml.o: in function `fx_r':
codeml.c:(.text+0x6d203): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `lfunRates':
codeml.c:(.text+0x6dadd): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x6e0d4): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x6e83f): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x6f016): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x6f3e6): undefined reference to `sqrt'
/usr/bin/ld: codeml.o: in function `lfunAdG':
codeml.c:(.text+0x6f4ea): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x6f79c): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x6fba0): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `lfun':
codeml.c:(.text+0x70549): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x70758): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x70769): undefined reference to `exp'
/usr/bin/ld: codeml.o: in function `CUDA_lfundG':
codeml.c:(.text+0x70a5d): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x70c86): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x70ca8): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x70cf8): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x70d08): undefined reference to `exp'
/usr/bin/ld: codeml.o: in function `lfundG':
codeml.c:(.text+0x710ad): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x712d6): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x712f8): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x71348): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x71358): undefined reference to `exp'
/usr/bin/ld: codeml.o: in function `AncestralMarginal':
codeml.c:(.text+0x71e3a): undefined reference to `pow'
/usr/bin/ld: codeml.o: in function `AncestralSeqs':
codeml.c:(.text+0x73c30): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `DatingHeteroData':
codeml.c:(.text+0x7a81b): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x7a842): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x7a869): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x7a88f): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x7a923): undefined reference to `sqrt'
/usr/bin/ld: codeml.o:codeml.c:(.text+0x7a9c7): more undefined references to `sqrt' follow
/usr/bin/ld: codeml.o: in function `distanceHKY85':
codeml.c:(.text+0x7adfd): undefined reference to `pow'
/usr/bin/ld: codeml.c:(.text+0x7ae44): undefined reference to `pow'
/usr/bin/ld: codeml.c:(.text+0x7ae85): undefined reference to `pow'
/usr/bin/ld: codeml.c:(.text+0x7b01e): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x7b03f): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x7b064): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `PairwiseCodon':
codeml.c:(.text+0x7d2b0): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x7d87d): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x7d894): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x7d9a4): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x7dafe): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x7db15): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x7dbe4): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x7dbf8): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x7dc9b): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x7dce0): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x7e0a2): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x7e167): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x7e1b0): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x7e242): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x7e288): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x7e2fa): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x7e311): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x7eefa): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x7ef2d): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x7ef5d): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x7ef94): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x7efc8): undefined reference to `sqrt'
/usr/bin/ld: codeml.o:codeml.c:(.text+0x7f005): more undefined references to `sqrt' follow
/usr/bin/ld: codeml.o: in function `get_grid_para_like_M2M8':
codeml.c:(.text+0x81762): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x8195b): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x81c69): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `lfunNSsites_M2M8':
codeml.c:(.text+0x82dd2): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x82f6d): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x83563): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x8363b): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x83975): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x8414f): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x84418): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x84808): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x8483b): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x848a2): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x848d1): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x84905): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x84923): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x849b2): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x84a0a): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x84a6b): undefined reference to `exp'
/usr/bin/ld: codeml.o:codeml.c:(.text+0x84aea): more undefined references to `exp' follow
/usr/bin/ld: codeml.o: in function `lfunNSsites_M2M8':
codeml.c:(.text+0x851ca): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x85774): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x8578b): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x857a7): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x857bd): undefined reference to `sqrt'
/usr/bin/ld: codeml.o:codeml.c:(.text+0x857d8): more undefined references to `sqrt' follow
/usr/bin/ld: codeml.o: in function `get_grid_para_like_ACD':
codeml.c:(.text+0x8643b): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x8670b): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x867bf): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `lfunNSsites_ACD':
codeml.c:(.text+0x88f6c): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x8a142): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x8a361): undefined reference to `log'
/usr/bin/ld: codeml.c:(.text+0x8a3b1): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x8a987): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x8abbb): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x8b283): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x8b299): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x8b2c3): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x8b2d9): undefined reference to `sqrt'
/usr/bin/ld: codeml.c:(.text+0x8b2f2): undefined reference to `sqrt'
/usr/bin/ld: codeml.o:codeml.c:(.text+0x8b308): more undefined references to `sqrt' follow
/usr/bin/ld: codeml.o: in function `lfunNSsites_rate':
codeml.c:(.text+0x8b6e3): undefined reference to `exp'
/usr/bin/ld: codeml.c:(.text+0x8ba84): undefined reference to `log'
/usr/bin/ld: codeml.o: in function `Forestry':
codeml.c:(.text+0x8e4af): undefined reference to `sqrt'
/usr/bin/ld: codeml.o: in function `logistic_transformation':
codeml.c:(.text+0x677b4): undefined reference to `exp'
/usr/bin/ld: cuda-codeml.o: in function `__cudaSafeCall(cudaError, char const*, int) [clone .part.0] [clone .constprop.0]':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x6b): undefined reference to `cudaGetErrorString'
/usr/bin/ld: cuda-codeml.o: in function `kernelConditionalPNodeTipClean(int, int, int, int, double const*, char const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x198): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1cb): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `kernelConditionalPNodeTipCleanFirst(int, int, int, int, double const*, char const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2e8): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x31b): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `kernelConditionalPNodeTipUnclean(int, int, int, int, double const*, char const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x438): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x46b): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `kernelConditionalPNodeTipUncleanFirst(int, int, int, int, double const*, char const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x588): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x5bb): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `kernelConditionalPNodeInternal(int, int, int, int, double const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x6b5): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x6e5): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `kernelConditionalPNodeInternalFirst(int, int, int, int, double const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x7d5): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x805): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `kernelNodeScale(int, int, int, int, double*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x8f5): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x925): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `kernelCalcFhK(int, int, double const*, double const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x9ff): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0xa2f): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `kernelPMatExptRoot(double const*, int const*, double const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0xaff): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0xb2f): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `kernelPMatUVRoot(int const*, double const*, double const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0xbff): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0xc2f): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `callKernelConditionalPNodeTipClean(int, int, int, int, int)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0xd09): undefined reference to `__cudaPushCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0xd16): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0xd51): undefined reference to `__cudaPushCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0xe32): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0xe69): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0xf51): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0xf88): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0xf96): undefined reference to `cudaGetErrorString'
/usr/bin/ld: cuda-codeml.o: in function `callKernelConditionalPNodeTipUnclean(int, int, int, int, int)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1089): undefined reference to `__cudaPushCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1096): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x10d1): undefined reference to `__cudaPushCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x11b2): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x11e9): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x12d1): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1308): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1316): undefined reference to `cudaGetErrorString'
/usr/bin/ld: cuda-codeml.o: in function `callKernelConditionalPNodeInternal(int, int, int, int, int)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1405): undefined reference to `__cudaPushCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1412): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1451): undefined reference to `__cudaPushCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1524): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x155b): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x163b): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1672): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1680): undefined reference to `cudaGetErrorString'
/usr/bin/ld: cuda-codeml.o: in function `callKernelNodeScale(int, int, int, int, int)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1769): undefined reference to `__cudaPushCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1837): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1840): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x189b): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x18ab): undefined reference to `cudaGetErrorString'
/usr/bin/ld: cuda-codeml.o: in function `callKernelCalcFhK(int, int, int)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x195f): undefined reference to `__cudaPushCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1a20): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1a29): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1a83): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1a93): undefined reference to `cudaGetErrorString'
/usr/bin/ld: cuda-codeml.o: in function `callKernelPMatUVRootAll(int)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1b16): undefined reference to `cudaMemcpy'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1b23): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1b55): undefined reference to `cudaMemcpy'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1b62): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1b94): undefined reference to `cudaMemcpy'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1ba1): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1bf1): undefined reference to `__cudaPushCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1bfe): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1c3e): undefined reference to `__cudaPushCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1c4b): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1d1b): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1d52): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1e0b): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1e42): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1e5c): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1e9d): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1ec7): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1edf): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1f07): undefined reference to `cudaGetErrorString'
/usr/bin/ld: cuda-codeml.o: in function `deviceInit(int)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1f48): undefined reference to `cudaSetDevice'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1f55): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1f7f): undefined reference to `cudaMemcpyToSymbol'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1f8c): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1fb6): undefined reference to `cudaMemcpyToSymbol'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1fc3): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1fed): undefined reference to `cudaMemcpyToSymbol'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x1ffa): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2024): undefined reference to `cudaMemcpyToSymbol'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2031): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x206b): undefined reference to `cudaMemcpyToSymbol'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2078): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x20a2): undefined reference to `cudaMemcpyToSymbol'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x20af): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x20d9): undefined reference to `cudaMemcpyToSymbol'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x20e6): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2110): undefined reference to `cudaMemcpyToSymbol'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x211d): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2147): undefined reference to `cudaMemcpyToSymbol'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2154): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2187): undefined reference to `cudaMalloc'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2194): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x21e0): undefined reference to `cudaMemcpy'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x21f0): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x222b): undefined reference to `cudaMalloc'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2238): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2268): undefined reference to `cudaMalloc'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2275): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x22a1): undefined reference to `cudaMemset'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x22ae): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x22d2): undefined reference to `cudaMalloc'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x22df): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2308): undefined reference to `cudaMalloc'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2315): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2333): undefined reference to `cudaMalloc'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2340): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2369): undefined reference to `cudaMalloc'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2376): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x239a): undefined reference to `cudaMalloc'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x23a7): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x23cb): undefined reference to `cudaMalloc'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x23d8): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x240c): undefined reference to `cudaStreamCreate'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x241b): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2476): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x24b7): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x24f7): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2513): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x252a): undefined reference to `cudaGetErrorString'
/usr/bin/ld: cuda-codeml.o:tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2545): more undefined references to `cudaGetErrorString' follow
/usr/bin/ld: cuda-codeml.o: in function `deviceFreeAll(int)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2cb5): undefined reference to `cudaStreamDestroy'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2cc4): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2cea): undefined reference to `cudaFree'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2cf7): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2d11): undefined reference to `cudaFree'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2d1e): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2d38): undefined reference to `cudaFree'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2d45): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2d5f): undefined reference to `cudaFree'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2d6c): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2d86): undefined reference to `cudaFree'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2d93): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2dad): undefined reference to `cudaFree'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2dba): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2dd4): undefined reference to `cudaFree'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2de1): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2dfb): undefined reference to `cudaFree'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2e08): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2e24): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2e64): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2ea5): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2ebd): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2ee1): undefined reference to `cudaGetErrorString'
/usr/bin/ld: cuda-codeml.o:tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x2f05): more undefined references to `cudaGetErrorString' follow
/usr/bin/ld: cuda-codeml.o: in function `nodeScale(int, int, int, int)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x33b5): undefined reference to `__cudaPushCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3483): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x348c): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x34eb): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x34fb): undefined reference to `cudaGetErrorString'
/usr/bin/ld: cuda-codeml.o: in function `schedule(int, int, int)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x35f8): undefined reference to `cudaStreamSynchronize'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3605): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x36d2): undefined reference to `__cudaPushCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x37ab): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3800): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3807): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3819): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x38a1): undefined reference to `cudaDeviceSynchronize'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x38ae): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3904): undefined reference to `__cudaPushCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3911): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3959): undefined reference to `cudaMemcpy'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3966): undefined reference to `cudaGetLastError'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3a5b): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3a9e): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3ab0): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3ad3): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3b15): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3b41): undefined reference to `cudaGetErrorString'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3b68): undefined reference to `cudaGetErrorString'
/usr/bin/ld: cuda-codeml.o: in function `__device_stub__Z30kernelConditionalPNodeTipCleaniiiiPKdPKcPd(int, int, int, int, double const*, char const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3ce8): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3d1b): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `__device_stub__Z35kernelConditionalPNodeTipCleanFirstiiiiPKdPKcPd(int, int, int, int, double const*, char const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3e38): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3e6b): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `__device_stub__Z32kernelConditionalPNodeTipUncleaniiiiPKdPKcPd(int, int, int, int, double const*, char const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3f88): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x3fbb): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `__device_stub__Z37kernelConditionalPNodeTipUncleanFirstiiiiPKdPKcPd(int, int, int, int, double const*, char const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x40d8): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x410b): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `__device_stub__Z30kernelConditionalPNodeInternaliiiiPKdPd(int, int, int, int, double const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x4208): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x4238): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `__device_stub__Z35kernelConditionalPNodeInternalFirstiiiiPKdPd(int, int, int, int, double const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x4328): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x4358): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `__device_stub__Z15kernelNodeScaleiiiiPdS_(int, int, int, int, double*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x4448): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x4478): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `__device_stub__Z13kernelCalcFhKiiPKdS0_Pd(int, int, double const*, double const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x4552): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x4582): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `__device_stub__Z18kernelPMatExptRootPKdPKiS0_Pd(double const*, int const*, double const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x4652): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x4682): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `__device_stub__Z16kernelPMatUVRootPKiPKdS2_Pd(int const*, double const*, double const*, double*)':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x4752): undefined reference to `__cudaPopCallConfiguration'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x4782): undefined reference to `cudaLaunchKernel'
/usr/bin/ld: cuda-codeml.o: in function `__cudaUnregisterBinaryUtil()':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text+0x5c): undefined reference to `__cudaUnregisterFatBinary'
/usr/bin/ld: cuda-codeml.o: in function `__sti____cudaRegisterAll()':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text.startup+0xd): undefined reference to `__cudaRegisterFatBinary'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text.startup+0x41): undefined reference to `__cudaRegisterFunction'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text.startup+0x6f): undefined reference to `__cudaRegisterFunction'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text.startup+0x9d): undefined reference to `__cudaRegisterFunction'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text.startup+0xcb): undefined reference to `__cudaRegisterFunction'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text.startup+0xf9): undefined reference to `__cudaRegisterFunction'
/usr/bin/ld: cuda-codeml.o:tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text.startup+0x127): more undefined references to `__cudaRegisterFunction' follow
/usr/bin/ld: cuda-codeml.o: in function `__sti____cudaRegisterAll()':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text.startup+0x209): undefined reference to `__cudaRegisterVar'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text.startup+0x231): undefined reference to `__cudaRegisterVar'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text.startup+0x259): undefined reference to `__cudaRegisterVar'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text.startup+0x282): undefined reference to `__cudaRegisterVar'
/usr/bin/ld: tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text.startup+0x2ac): undefined reference to `__cudaRegisterVar'
/usr/bin/ld: cuda-codeml.o:tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text.startup+0x2d5): more undefined references to `__cudaRegisterVar' follow
/usr/bin/ld: cuda-codeml.o: in function `__sti____cudaRegisterAll()':
tmpxft_000c2136_00000000-6_cuda-codeml.cudafe1.cpp:(.text.startup+0x35e): undefined reference to `__cudaRegisterFatBinaryEnd'
/usr/bin/ld: tools.o: in function `IncompleteGamma.part.0':
tools.c:(.text+0x47): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x62): undefined reference to `exp'
/usr/bin/ld: tools.o: in function `PMatUVRoot':
tools.c:(.text+0x1836): undefined reference to `exp'
/usr/bin/ld: tools.o: in function `pijJC69':
tools.c:(.text+0x2231): undefined reference to `exp'
/usr/bin/ld: tools.o: in function `PMatK80':
tools.c:(.text+0x235f): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x2481): undefined reference to `exp'
/usr/bin/ld: tools.o:tools.c:(.text+0x2649): more undefined references to `exp' follow
/usr/bin/ld: tools.o: in function `PickExtreme':
tools.c:(.text+0x48b6): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x4906): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `distance':
tools.c:(.text+0x88b0): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `norm':
tools.c:(.text+0x8eb0): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `f_and_x':
tools.c:(.text+0x99ac): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x99cb): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x99ef): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x9a13): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x9a37): undefined reference to `exp'
/usr/bin/ld: tools.o:tools.c:(.text+0x9a5b): more undefined references to `exp' follow
/usr/bin/ld: tools.o: in function `f_and_x':
tools.c:(.text+0xa014): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0xa02a): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0xa044): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0xa05e): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0xa078): undefined reference to `log'
/usr/bin/ld: tools.o:tools.c:(.text+0xa092): more undefined references to `log' follow
/usr/bin/ld: tools.o: in function `bigexp':
tools.c:(.text+0xa276): undefined reference to `pow'
/usr/bin/ld: tools.o: in function `reflect':
tools.c:(.text+0xa560): undefined reference to `fmod'
/usr/bin/ld: tools.o: in function `ResetFinetuneSteps':
tools.c:(.text+0xaeef): undefined reference to `tan'
/usr/bin/ld: tools.c:(.text+0xaf09): undefined reference to `tan'
/usr/bin/ld: tools.c:(.text+0xaf84): undefined reference to `tan'
/usr/bin/ld: tools.c:(.text+0xaf9e): undefined reference to `tan'
/usr/bin/ld: tools.c:(.text+0xb08c): undefined reference to `tan'
/usr/bin/ld: tools.o:tools.c:(.text+0xb0a6): more undefined references to `tan' follow
/usr/bin/ld: tools.o: in function `rndNormal':
tools.c:(.text+0xbf0f): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0xbf69): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `rndBactrianTriangle':
tools.c:(.text+0xc2db): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0xc311): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `rndBactrianLaplace':
tools.c:(.text+0xc3b4): undefined reference to `log'
/usr/bin/ld: tools.o: in function `rndAirplane':
tools.c:(.text+0xca7a): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `rndStrawhat':
tools.c:(.text+0xce40): undefined reference to `pow'
/usr/bin/ld: tools.o: in function `rndloglogistic':
tools.c:(.text+0xcf1a): undefined reference to `log'
/usr/bin/ld: tools.o: in function `rndTriangle':
tools.c:(.text+0xd0a1): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0xd0ce): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `rndLaplace':
tools.c:(.text+0xd164): undefined reference to `log'
/usr/bin/ld: tools.o: in function `rndt2':
tools.c:(.text+0xd27b): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `rndt4':
tools.c:(.text+0xd443): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0xd46d): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `rndgamma':
tools.c:(.text+0xd590): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0xd5a1): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0xd67c): undefined reference to `pow'
/usr/bin/ld: tools.c:(.text+0xd6ce): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `QuantileNormal':
tools.c:(.text+0xf29f): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0xf391): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `PDFNormal':
tools.c:(.text+0xf408): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0xf439): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `logPDFNormal':
tools.c:(.text+0xf487): undefined reference to `log'
/usr/bin/ld: tools.o: in function `CDFNormal':
tools.c:(.text+0xf5b3): undefined reference to `exp'
/usr/bin/ld: tools.o: in function `logCDFNormal':
tools.c:(.text+0xf72f): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0xf7ac): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0xf7f7): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0xf88d): undefined reference to `log'
/usr/bin/ld: tools.o: in function `PDFloglogistic':
tools.c:(.text+0xf91b): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0xf934): undefined reference to `exp'
/usr/bin/ld: tools.o: in function `PDFlogt2':
tools.c:(.text+0xf98b): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0xfa09): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `PDFt2':
tools.c:(.text+0xfa99): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `PDFt4':
tools.c:(.text+0xfaf3): undefined reference to `pow'
/usr/bin/ld: tools.o: in function `PDFSkewN':
tools.c:(.text+0xfb62): undefined reference to `exp'
/usr/bin/ld: tools.o: in function `logPDFSkewN':
tools.c:(.text+0xfbec): undefined reference to `log'
/usr/bin/ld: tools.o: in function `lnStirlingS2':
tools.c:(.text+0x10074): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x100e2): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x10159): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x101c4): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1027a): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x1028b): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x10298): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x102eb): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x102fc): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x10334): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x10423): undefined reference to `log'
/usr/bin/ld: tools.o:tools.c:(.text+0x1049d): more undefined references to `log' follow
/usr/bin/ld: tools.o: in function `rndpoisson':
tools.c:(.text+0x1096f): undefined reference to `tan'
/usr/bin/ld: tools.c:(.text+0x10a34): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x10b7d): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x10be9): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x10c05): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `PDFt':
tools.c:(.text+0x10ca8): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x10cc0): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x10d31): undefined reference to `log'
/usr/bin/ld: tools.o: in function `QuantileChi2.part.0':
tools.c:(.text+0x10db7): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x10e43): undefined reference to `pow'
/usr/bin/ld: tools.c:(.text+0x10e89): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x10ea8): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x10edf): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x10f8a): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x110cf): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x11100): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1139d): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x113c6): undefined reference to `pow'
/usr/bin/ld: tools.c:(.text+0x1140f): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `CDFBeta.part.0':
tools.c:(.text+0x11527): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x11538): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x117a2): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x117cb): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x118ec): undefined reference to `log'
/usr/bin/ld: tools.o:tools.c:(.text+0x11921): more undefined references to `log' follow
/usr/bin/ld: tools.o: in function `CDFBeta.part.0':
tools.c:(.text+0x119a5): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x11ce9): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x11d8b): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x1204e): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1241f): undefined reference to `log'
/usr/bin/ld: tools.o: in function `QuantileBeta.part.0':
tools.c:(.text+0x126d0): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x127d3): undefined reference to `pow'
/usr/bin/ld: tools.c:(.text+0x12903): undefined reference to `pow'
/usr/bin/ld: tools.c:(.text+0x12a02): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x12a1d): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x12a45): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1304b): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1334d): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x1335e): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1339a): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x133ab): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x137e1): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x1384b): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x13887): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `PDFSkewT':
tools.c:(.text+0x15a53): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x15a80): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x15b1f): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x15b38): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x15c0c): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x15c60): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `PDFGamma':
tools.c:(.text+0x15ce3): undefined reference to `pow'
/usr/bin/ld: tools.c:(.text+0x15d29): undefined reference to `exp'
/usr/bin/ld: tools.o: in function `logPriorRatioGamma':
tools.c:(.text+0x15d94): undefined reference to `log'
/usr/bin/ld: tools.o: in function `PDFinvGamma':
tools.c:(.text+0x15e23): undefined reference to `pow'
/usr/bin/ld: tools.c:(.text+0x15e69): undefined reference to `exp'
/usr/bin/ld: tools.o: in function `DiscreteBeta':
tools.c:(.text+0x16272): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x16eef): undefined reference to `log'
/usr/bin/ld: tools.o: in function `LBinormal':
tools.c:(.text+0x1a6ce): undefined reference to `asin'
/usr/bin/ld: tools.c:(.text+0x1a705): undefined reference to `sin'
/usr/bin/ld: tools.c:(.text+0x1a72f): undefined reference to `sin'
/usr/bin/ld: tools.c:(.text+0x1a775): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1a7d7): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1a832): undefined reference to `sin'
/usr/bin/ld: tools.c:(.text+0x1a855): undefined reference to `sin'
/usr/bin/ld: tools.c:(.text+0x1a89d): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1a8ff): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1a94d): undefined reference to `sin'
/usr/bin/ld: tools.c:(.text+0x1a970): undefined reference to `sin'
/usr/bin/ld: tools.c:(.text+0x1a9bb): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1aa22): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1aa64): undefined reference to `sin'
/usr/bin/ld: tools.c:(.text+0x1aa8e): undefined reference to `sin'
/usr/bin/ld: tools.c:(.text+0x1aada): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1ab36): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1ad73): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1adb1): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1ae90): undefined reference to `exp'
/usr/bin/ld: tools.o:tools.c:(.text+0x1aecf): more undefined references to `exp' follow
/usr/bin/ld: tools.o: in function `LBinormal':
tools.c:(.text+0x1b22a): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x1b2b9): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x1b32e): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `logLBinormal':
tools.c:(.text+0x1c691): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1c6a7): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1c6c1): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1c821): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x1ca55): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1cb2c): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1cb71): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1cca3): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1cd37): undefined reference to `exp'
/usr/bin/ld: tools.o:tools.c:(.text+0x1cd53): more undefined references to `exp' follow
/usr/bin/ld: tools.o: in function `logLBinormal':
tools.c:(.text+0x1cdc7): undefined reference to `asin'
/usr/bin/ld: tools.c:(.text+0x1ce35): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1ce7e): undefined reference to `sin'
/usr/bin/ld: tools.c:(.text+0x1cea1): undefined reference to `sin'
/usr/bin/ld: tools.c:(.text+0x1cf38): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1cf83): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1cf99): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1cfe3): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1d011): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x1d033): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x1d070): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `probBinomialDistribution':
tools.c:(.text+0x1d3ea): undefined reference to `pow'
/usr/bin/ld: tools.o: in function `probBinomial':
tools.c:(.text+0x1d67b): undefined reference to `pow'
/usr/bin/ld: tools.c:(.text+0x1d69d): undefined reference to `pow'
/usr/bin/ld: tools.c:(.text+0x1d6cb): undefined reference to `pow'
/usr/bin/ld: tools.c:(.text+0x1d76e): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x1d792): undefined reference to `pow'
/usr/bin/ld: tools.c:(.text+0x1d7c2): undefined reference to `pow'
/usr/bin/ld: tools.o: in function `probBetaBinomial':
tools.c:(.text+0x1d8f5): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x1da1f): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x1db57): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x1dbca): undefined reference to `exp'
/usr/bin/ld: tools.o: in function `PDFBeta':
tools.c:(.text+0x1dcd2): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x1dcef): undefined reference to `log'
/usr/bin/ld: tools.o: in function `GetIndexTernary':
tools.c:(.text+0x21ec1): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `Binomial':
tools.c:(.text+0x22033): undefined reference to `log'
/usr/bin/ld: tools.o: in function `BinomialK':
tools.c:(.text+0x22604): undefined reference to `log'
/usr/bin/ld: tools.o: in function `CholeskyDecomp':
tools.c:(.text+0x277c0): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `HouseholderRealSym':
tools.c:(.text+0x29c3d): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x29d44): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `EigenTridagQLImplicit':
tools.c:(.text+0x2a61f): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x2a6be): undefined reference to `sqrt'
/usr/bin/ld: tools.o:tools.c:(.text+0x2a744): more undefined references to `sqrt' follow
/usr/bin/ld: tools.o: in function `density2d':
tools.c:(.text+0x30072): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0x3012f): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x3020a): undefined reference to `pow'
/usr/bin/ld: tools.c:(.text+0x3028e): undefined reference to `pow'
/usr/bin/ld: tools.c:(.text+0x30313): undefined reference to `pow'
/usr/bin/ld: tools.c:(.text+0x30396): undefined reference to `pow'
/usr/bin/ld: tools.c:(.text+0x3041a): undefined reference to `pow'
/usr/bin/ld: tools.o:tools.c:(.text+0x3049f): more undefined references to `pow' follow
/usr/bin/ld: tools.o: in function `density2d':
tools.c:(.text+0x31edc): undefined reference to `exp'
/usr/bin/ld: tools.c:(.text+0x321b8): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `Eff_IntegratedCorrelationTime':
tools.c:(.text+0x3303d): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x330b1): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `DescriptiveStatistics':
tools.c:(.text+0x34a3e): undefined reference to `pow'
/usr/bin/ld: tools.c:(.text+0x355c7): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x35611): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x3563b): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `H_end':
tools.c:(.text+0x35bba): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x35c1b): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `gradient':
tools.c:(.text+0x362a4): undefined reference to `pow'
/usr/bin/ld: tools.o: in function `nls2':
tools.c:(.text+0x39f1a): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x39f77): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x39fd8): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `LineSearch2':
tools.c:(.text+0x3f9f8): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x3fa2a): undefined reference to `sqrt'
/usr/bin/ld: tools.o:tools.c:(.text+0x42339): more undefined references to `sqrt' follow
/usr/bin/ld: tools.o: in function `gradientB':
tools.c:(.text+0x42893): undefined reference to `pow'
/usr/bin/ld: tools.o: in function `ming2':
tools.c:(.text+0x4a1bb): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x4a1dd): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x4a203): undefined reference to `sqrt'
/usr/bin/ld: tools.c:(.text+0x4a3a5): undefined reference to `sqrt'
/usr/bin/ld: tools.o: in function `ming1':
tools.c:(.text+0x4ea50): undefined reference to `sqrt'
/usr/bin/ld: tools.o:tools.c:(.text+0x4eaa3): more undefined references to `sqrt' follow
/usr/bin/ld: tools.o: in function `rndloglogistic':
tools.c:(.text+0xceed): undefined reference to `exp'
/usr/bin/ld: tools.o: in function `rndlogistic':
tools.c:(.text+0xcf7e): undefined reference to `log'
/usr/bin/ld: tools.c:(.text+0xcf9b): undefined reference to `log'
/usr/bin/ld: tools.o: in function `rndCauchy':
tools.c:(.text+0xcfde): undefined reference to `tan'
/usr/bin/ld: tools.o: in function `rndlogt2':
tools.c:(.text+0xd2e8): undefined reference to `exp'
/usr/bin/ld: tools.o: in function `logCDFNormal':
tools.c:(.text+0xf8b2): undefined reference to `log'
/usr/bin/ld: tools.o: in function `lnStirlingS2':
tools.c:(.text+0x10539): undefined reference to `log'
/usr/bin/ld: tools.o: in function `LnGamma':
tools.c:(.text+0x107eb): undefined reference to `log'
/usr/bin/ld: tools.o: in function `PDFBeta':
tools.c:(.text+0x1dd87): undefined reference to `exp'
collect2: error: ld returned 1 exit status
make: *** [Makefile:87: CuCodeML] Error 1

Do you have any ideas what I can do here?

Cheers!

[kim2039]

Yes, I have same issues. But I cannot resolve this.